Transposed
by Fifth Horseman
Summary: One change, be it big or small, can set in motion different circumstances that drastically change things. Hopefully for the better.
1. Chapter 1

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

This story was originally started about nine years ago in an effort to start writing longer material. It sat largely neglected and seldom visited until about two years ago or so and the bulk of it has been written since then.

It was not always a pleasant journey. Bouts of apathy about life in general and episodes of what may well have been depression took a toll on me and weeks would go by where I didn't even look at this. Add a few instances of outright frustration with this story and what should have been done in a year stretched to two or more.

Despite my love/hate relationship with this story I do think it came out well. In this story I have used elements from both the anime and the manga where I thought they fit the scenes better. I actually like some of the subtle differences of the manga characters better. I may have also tweaked a few little things with characters here and there.

It will probably be updated twice a week...I am looking at Mondays and Thursdays for release dates.

Reviews are encouraged and welcome. I try to respond to most when possible. I haven't decided yet if I am going to respond to the reviews that have no reply link at the start of the next chapter or not. It might depend upon what the review said.

With that said, I hope you enjoy my return to the Eva section, it's been a while since I posted anything here. Hope you enjoy it.

 **Transposed**

 _ **Chapter 1**_

On a massive steel gantry platform, deep inside the part of the Tokyo-3 NERV complex that was known as Central Dogma, a beautiful, purple haired woman wearing a short, sleeveless black dress and a red leather uniform jacket sat despondently on the cold metal floor in a puddle of LCL, her bare legs and most of said dress soaked with the putrid liquid.

From a pair of normally soft and warm brown eyes, tears flowed freely leaving them swollen and bloodshot. She didn't care who saw her like this or what they thought of her for it, or what it did to her professional reputation. None of that mattered to her in the slightest right now. In front of her, locked down and restrained in its massive gantry and swathed in cables and vast arrays of monitoring equipment was the giant armoured inhuman creation known as Shogoki. Evangelion, Unit 01.

The Berserker.

The damage sustained in its last battle one month earlier had been repaired and the armour it had shed had been replaced. Damage taken in a battle where at its end the man made monster gained awareness and as the still living Angel known as Zeruel lay twitching and writhing beneath it, ate its S2 organ in a bloody and gruesome display of savage and animalistic butchery. Its massive core was still exposed however, as Dr. Ritsuko Akagi and her staff of technicians tried seemingly in vain to recover the beast's reluctant pilot, fourteen year old Shinji Ikari, who had been absorbed into the living weapon during that last horrifying battle.

The LCL soaked woman crying on the cold steel was many things to Shinji Ikari. Major Misato Katsuragi was his commanding officer, his guardian, and his friend. She had grown quite attached to the young man in the months he had been in her care and the thirty days that had passed since he had been absorbed into the beast's core had been extremely hard on her, adding fresh wounds to her already scarred and damaged soul.

Her job as NERV's Head of Operations gave her enough headaches, worries, and stress as it was, the necessity of having to send children out to fight monsters would do that, but recent events had added to the intense pressure she felt weighing down upon her nearly every hour of the day. She had been finding out just how little she really knew of the overall picture of what went on at NERV and it disturbed her a great deal.

On top of that her other charge Asuka was being exceedingly petulant and defiant again, something that her already frayed nerves were having a great deal of trouble coping with. She was being whiny and resentful at the fact that she had been saved once more by 'idiot Shinji', and she seemed to be totally unsympathetic to his current plight and it had been the source of several very loud and very nasty arguments between the two of them, giving her no respite from the stress even at home.

Asuka didn't seem to care in the least about her fellow pilot and housemate, but as the days since the Evangelion assimilated Shinji into itself wore on, Misato had come to realize just how truly close to her own heart the shy and withdrawn young man had become. Even more so than when he was swallowed up by the Twelfth Angel. She had come to the realization that if she lost Shinji it would be the end of her world and it would destroy her completely. He was the best thing in her life and nearly the only thing that she had to cling to in order to maintain the shreds her own fraying sanity.

When Shinji's father, a title the rotten bastard most certainly didn't deserve and only maintained because of genetics, had summoned the son he had abandoned ten years earlier to Tokyo 3, Misato had been the one who had picked him up and rushed him to NERV. She had truly felt sorry for the kid. All he had wanted was his father's love and approval and what he got was a gruff ultimatum. Summoned only because there was a specific need for his presence, because he was now useful to the bastard who had abandoned him all those lonely years ago. He was told to pilot the Eva or go away.

He was manipulated through his sympathy for a badly injured Rei Ayanami, a girl he had never even seen before, to get into the pilot's seat so that she wouldn't have to. Even after the terrified boy had fought and defeated the Angel, with plenty of help from a berserk Unit 01, Commander Ikari still couldn't muster even the slightest show of pride or gratitude towards his own son. Not even the smallest hint of praise was directed Shinji's way. He had even arranged for the boy to live on his own, for all intents and purposes abandoning him once again and to lodgings that weren't fit for rats to live in. Misato hadn't hesitated and took him into her home, as much to alleviate her own loneliness and her aching need for companionship as for his own well being.

Over the time they had been living together their relationship had steadily grown stronger. Shinji had been slowly becoming less withdrawn and more outgoing, her teasing ways and scantily clad antics serving to loosen him up ever so slightly beyond the embarrassment they caused him and letting him know that maybe someone really did give a damn about him after all in this miserable world. Their relationship had its good days and bad days, a good lot of it due to his battles against the Angels and the ways it affected his fragile psyche, but she was proud of even the small steps forward he was taking and she could only hope that she had been responsible in some small way for it. She knew that she was hardly the ideal of a good role model, but she genuinely cared about him and she wanted to see him become stronger and be able to stand up for himself.

Words couldn't say how genuinely proud she was of him for continuing to pilot Unit 01, something he truly despised doing. While he really did want to protect people he piloted more out of a sense of obligation and a quest for an identity than commitment to a cause, and he continued to do it even though it caused him a great deal of pain. The kid had probably spent almost as much time in the hospital as out of it since he came to Tokyo 3, but he kept getting back into the purple behemoth and saving all of them from the Angels again and again.

He was a lot tougher than he gave himself credit for and he was certainly far braver than he thought he was. If only he could see it for himself. He kept calling himself a coward, but a coward wouldn't keep coming back to the fight and defeating the enemy. Whether he could see it or not, he was a hero. A reluctant one sure enough, but those were the type who often displayed heroism in its truest form. They didn't seek glory for their actions, they only did what needed to be done because someone had to do it.

Misato had come to realize that she could no longer see her life without Shinji in it in some capacity. He really was a good kid and to her own embarrassment she had to admit that he looked after her a lot more than she looked after him. He had come to accept her for who she was, warts and all, though she didn't know how long that would last if he ever saw the worst of her behaviour and he seemed to genuinely care a great deal about her.

The nature of her feelings for him were a source of personal struggle for her at times. She was a surrogate mother, a big sister, and a friend to him, and to be totally honest, if their ages and circumstances were different their relationship would most definitely be something a lot less wholesome. But that wasn't the reality of it. They were a big part of each others lives and it had become apparent to Misato that it was a part of her life she could no longer live without. Perhaps it was just her loneliness talking, but she needed him. He was her family and the fact that he had been lost to her for the last month was slowly and surely killing her.

* * *

Up in the control room, Ritsuko Akagi watched her friend through the observation windows as she washed down a handful of aspirin with yet another cup of the horrible, industrial strength, and quite possibly toxic concoction that passed for coffee on the command deck. Their most recent and best attempt to recover Shinji from Unit 01's core had failed and she was tired. Actually, she had passed tired a long time ago and was now somewhere on the far downhill side of total exhausted.

With little success to show for it, she and her crew had been trying for a month to find a way to get Unit 01 to give up its shy and reluctant young pilot and they were running out of options. The telemetry and the sequence of events from their last attempt to retrieve him had left her with no other conclusion than to think that Shinji simply didn't want to come back. After everything the boy had been through she could understand it if that was the case and he didn't want to return. They had placed the weight of the entire world on his slim, untrained and unprepared young shoulders, and while he had managed to carry that weight thus far, he hadn't done so without sustaining significant damage in return.

If he had actually decided to stay within the Eva and thus was able to finally run away for good, she really couldn't say that she would hold it against him. But there were forces at work to whom that outcome would be most unacceptable and although her reasons were different than those of Commander Ikari, Misato had made it painfully clear that she expected her to do anything and everything possible, and then some, to retrieve Shinji from within the belly of the beast that was Evangelion.

' _You've gotten way too close to him Misato,'_ she thought sadly. _'You're his commanding officer, it's your job to send him out to fight… and to die if necessary,… to protect the human race.'_

It wasn't that she didn't like Shinji, she did, he was a good enough kid and he tried hard despite the pain and discomfort his battles caused for him and the crippling nature of his past. Hell, if she had known that he could cook like he did she may well have taken him in herself and gotten the better of the two Ikari men by far in the process. But none of them could afford to be too attached to the pilots. She knew that made her sound like a cold, heartless bitch, but it was the hard and brutal truth of the situation they were in.

However, her conscience had been rearing its ugly head for the last month or so. She could have sworn she had beaten it into submission and buried it a long time ago, but apparently it was still alive and well and more than willing to start kicking her ass. After awakening from a long hibernation it had been forcing her to think about all of the things she had done and still continued to do.

Luckily, she was a hardcore workaholic and that usually was sufficient enough distraction to push her troublesome conscience aside, but that didn't seem to be working lately. She had been suffering from some rare moments of clarity about her situation recently and it weighed heavily on her mind. She found herself regretting a great many of the things that she had done under the guise of Project E and one of the things she was beginning to regret most of all was her so called relationship with Gendo Ikari.

She had been overwhelmed by the man from the very start. Her relationship with him filled the void of loneliness that she had seemed to carry within her for as long as she could remember. She had never been good with relationships so it came as a great boost to her that someone as important and as powerful as Gendo Ikari would be interested in her, let alone romantically so. However, she had only been seeing what she wanted to see and by the time she had realized that she was just another of his many tools, it was far too late. She was hooked. Leave it to her to be in love with a man that clearly didn't love her and was only using her for her expertise in his quest to be reunited with his dead wife.

There was no way she could ever compete with that, but his cult of personality had ensnared her just like it had her mother before her and she had no doubt that she too would meet a very bad end when her usefulness to him had run its due course. Had she really been so overwhelmingly desperate for someone to love her, for someone to notice her, that she was willing to not only overlook the things that he was doing but to be an active participant in it as well? How had she managed to sink to such abysmal depths?

Lately, she was really not liking what she saw staring back at her from the mirror every morning. She had been spending a lot of time recently thinking about who and what she had become and the shame was almost more than she could bear. All of the things she had been forced to do and all of the things she had done willingly and without question to aid his cause were beginning to catch up to her and were crushing her soul under their immense weight. She was damned if she knew how to get out from under it now.

One of her worst transgressions among the many she had committed, and the one that seemed to be hitting her the hardest these days, was the way she had treated Rei Ayanami. She didn't know why she had suddenly started to feel such guilt and remorse over her treatment of the hybrid girl. Maybe it was because of her waning love for Gendo and her realization of just what a monster he truly was, and what a monster she was well on her way to becoming. Maybe it was because of the way that Rei seemed to be so unaffected and oblivious on an emotional level, as if she wasn't even aware of her own mistreatment.

Considering the way she had been raised and how her behaviour had been directed and managed through both psychological means and the use of an array of pharmaceuticals, it was little wonder. Gendo had wanted to create an obedient, emotionless doll that would do exactly what he ordered her to do without question, and he had succeeded wonderfully. He had created a life simply so he could twist it to his own selfish ambitions. Something that she had played no small role in bringing about.

She had been so jealous of all the attention he paid to the girl that she ended up treating her with barely concealed contempt, as if she were nothing more than an inconvenient lab experiment that someone else had dumped into her lap. Rei herself had done absolutely nothing to deserve the treatment she received at her hands. She was probably the biggest victim of them all because she suffered at the hands of so many and it was doubtful that she even really knew it. Her newly resurgent conscience had been forcing her to start looking at the situation and the world at large from Rei's perspective. It had given her many sleepless nights and it left her feeling hollow and sickened and horribly ashamed of herself.

' _Maybe your way is better Misato,'_ she mused sadly as she continued to watch her distraught friend. _'At least you still have your humanity. I seem to have misplaced mine somewhere.'_

* * *

On another walkway far above the control room and the restrained monster, stood a blue haired, red eyed girl, dressed in a teal green and white school uniform. Rei Ayanami usually displayed little in the way of emotion. Despite what people thought of her she did indeed feel emotions, she just didn't quite know what to do with them, or how to accurately identify them, and she certainly didn't know what to do with them. Much of the time she simply had no capacity to care about them. But if anyone were to see her right now they would see an obvious and unmistakable look of worry on her face. She was very afraid for the fate of the one person she could truly call a friend. Perhaps the only real friend that she had.

Almost from the first moment that Shinji Ikari had entered her life he had begun to have an effect upon her. At first she was simply puzzled by it. When the attack of the Third Angel caused her to be knocked from her hospital gurney he had rushed to her aid and cradled her bleeding and broken body in his arms. Then, despite being scared half to death, he agreed to pilot the Eva so that she wouldn't have to. She didn't know why he would do such a thing. He didn't know her or know anything about her, yet he was willing to take the pain and risk his life so that she would not have to.

His accidental groping of her breast had left her feeling…unsettled. Perhaps because she had never been touched in such a fashion before and the sensation itself had been strange to her, though not altogether unpleasant. When he helped her out of the entry plug after they destroyed the Fifth Angel she noticed the warmth of his touch even through the material of her plug suit. It too was not displeasing. She had also smiled for him. Both the smile and the touch had affected her greatly, making her wish to be in his presence more often though she did not understand why.

The day she had asked him to stay and have tea with her at her apartment had been a uncommon occurrence for her. Somehow she felt compelled to be with him. When she burned herself on the kettle and he held her hand under the cool water to soothe it, the feeling was different from anything else she had experienced before. It was pleasant and somehow made her feel warm, even happy. It was all very confusing to her and from that moment on she knew she was no longer the same as she had been. She was starting to actually _feel_ and it was all because of the kindness of Shinji Ikari.

It caused her to spend a great deal of time thinking about her life and where it was going. She felt herself being drawn towards Shinji and away from the Commander. She found herself thinking of him now instead of the man who had created her and given her a purpose in life. She no longer wished to be an empty, emotionless puppet to a man whom she now realized had never truly cared for her as a person, but only as the tool he had created to serve his needs.

Her body may have been created in a laboratory and her soul may be that of Lilith, but she had made them her own. She was not a puppet or a doll or a tool. She was Rei Ayanami, inside and out, and she was beginning to figure out what _she_ wanted. She wanted to live. She wanted to feel. She wanted to experience life and know what it was to be happy and she wanted to discover it all with Shinji.

If only the beast would give him back.

She silently pleaded with it to let him go. In her mind she saw the bestial face of the true monster that lay beneath the armour. There was a part of them that was the same. They were both created of the flesh of Lilith. Her eyes closed in concentration, her mind sought out the purple Eva's consciousness.

' _I am you,"_ she began. _'You are myself. You are what used to be me.'_

' _Yes, you are me,'_ the beast responded, its voice tinged with annoyance. _'I am what used to be you. So then, why? Why do you interfere?'_

' _You can't,'_ Rei pleaded. _'Don't take Ikari-kun away. Give him back to me.'_

Inside the core, the beast seemed to consider this for a moment as it regarded the young boy who now fearfully struggled against it, its selfish and self serving disguise as his mother now gone because of the blue haired child's interference. Reluctantly it let him drift away, onward toward the waiting arms of his real mother. Suddenly, the beast transformed its appearance again to that of a beautiful woman with long, dark, flowing hair. That beautiful face though was now marred by a look of deep shame.

' _I have been selfish and thought only of myself,'_ the woman whispered. _'I have let the baser instincts of the beast override me again since going berserk against the Fourteenth and the process of assimilating its S2 organ is affecting my sense of self. I must refocus and maintain myself and my control, otherwise I am jeopardizing everything.'_ She seemed to pause and gather herself. _'No matter what I may do, the choice ultimately must be his. He is the key to it all. He always has been.'_

Rei could feel no malice in the entity's words. The soft voice sounded hopeful, yet sad at the same time. It puzzled her, but it didn't really matter that much just so long as it allowed Shinji to leave if he so chose to.

' _Come back Ikari….Shinji…please come back.'_

* * *

Back down on the gantry walkway, Misato was coming apart at the seams. Every moment for the last month she had hoped and prayed for Shinji's safe return and had drank herself stupid on many of those nights in grief and fear. For the last several hours she had been cursing the name of every deity she could think of because nothing had worked in the effort to bring her Shinji back to her.

She wasn't good at sitting around and waiting for others to accomplish things, especially when she could add nothing to the solution herself. She wanted so badly to be able to do something, anything at all to bring him back, to be an active part of the solution. But she knew that none of her tactical or martial abilities would make a difference here. This was Ritsuko's field of play and she had made it very clear what she expected of her old friend, but she could feel the cold hand of failure and helplessness clawing at her already damaged heart. Nothing had worked so far or shown much promise of success.

She had no idea what was going on with Shinji inside the Eva and that hurt her as much as his absence did. She couldn't imagine it being anything good. The Evangelion was a creation that they couldn't truly control, a reality that it had brutally driven home to them a month earlier when it had messily made a meal out of the Fourteenth Angel. The ugly truth was that they knew so little about the beast they had created, but they had no other choice but to use it. Was Shinji even still alive inside of its core? Was he aware of anything that was going on around him and that they were trying to get him back? Was he afraid? Was he in pain?

"You have to fight it Shinji," she said in a raspy, shaking voice. "You have to fight to get out of there. Don't let it take you away from me. Please Shinji-kun, don't leave me here all alone."

She buried her face in his empty white shirt which, along with the rest of his clothes, had been expelled from Unit 01's entry plug during the latest retrieval effort. Her tears flowed freely and heavily. It wasn't fair. As reluctant and as scared as he was, he was their champion. Their Slayer of Angels. He was _her_ champion. He wasn't the most talented, graceful, or willing fighter, but he got the job done and that was what mattered. Without him, not one of them would still be alive right now.

He was an innocent fourteen year old boy, saddened by the loss of his mother and made lonely and withdrawn by his heartless bastard of a father and those whose negligent care he was left in. He was a gentle soul who was forced to fight creatures he couldn't comprehend, in a weapon he could barely control. He didn't deserve this. Why had that monster taken him away from her? What did it want from him that he hadn't already given?

She raised her tear streaked face and looked up at Unit 01, screaming defiantly at it with all of her pain and rage. "What do you want with him you fucking monster! It wasn't enough for you to eat the last Angel so you had to take Shinji too?! You can't have him! I won't let you have him!" She stood and rushed to the unprotected core and started pounding it furiously with her fists until her knuckles were raw and bloody.

"Give him back to me! Give me back my Shinji!"

* * *

"She's out of her beer soaked mind!" Ritsuko exclaimed.

"Dr. Akagi!" Maya yelled. "There's an energy spike in Unit 01's core!"

"Misato! Get the hell away from there! Get away from the core!" Akagi screamed over the intercom.

"The core is glowing!" Shigeru reported. "Energy readings have gone off the scale! It frying all of the sensors."

Before any of them could take any action, the glow flared and Misato was gone, pulled right out of her clothes and into the core. The flash blinded the bridge crew, disrupting the majority of their instruments and sending alarms blaring.

Ritsuko squeezed her eyes shut tightly, then blinked rapidly several times, trying to clear her vision. When she could see again she was witness to a most unexpected sight. First, the naked body of Shinji Ikari was expelled gracelessly from the core, landing with a splash in the LCL and discarded clothing that covered the floor. As she ordered Maya to call for a medical team a much bigger surprise came. Another naked body was pushed out of the core. This one was a slim woman with brown hair.

"Oh my God!" Ritsuko gasped, as she laid eyes on the unconscious form of Yui Ikari.

* * *

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	2. Chapter 2

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

 **Transposed**

 _ **Chapter 2**_

 _ **Office of Gendo Ikari**_

In an instant his world had dramatically changed. From his usual pose, hands folded under his nose concealing his mouth and elbows resting on his desk, he watched the footage of the incident again for perhaps the tenth time, scarcely able to believe what he was seeing. It was a most unexpected turn of events, but one that was welcome nonetheless. It seemed that his carefully planned scenario would no longer be necessary. He had what he wanted and it was better than a hopeful merging of souls. His Yui was here, alive and in the flesh.

However, if there was one thing that Gendo Ikari had learned throughout his years of manipulations, political wrangling, and the fight against the Angels, it was to never, ever, take anything at face value. He was no stranger to tricks and deceptions and he would temper his joy at his wife's reappearance until he was sure that it wasn't a ruse. He could feel it in his bones that it was genuine, but he had to be sure.

Both Yui and his son were in isolation in NERV's medical complex and would stay there until every possible test could be done to confirm that it was really them and not a manifestation of an Angel. Only when it had been proven that there was no doubt to their identities and that there was no contamination present would he accept what his heart was telling him must be true. It had to be true.

"Fuyutsuki," he said to the older man standing next to him. "I want you to personally oversee and review the tests. If there is anything that seems off, even in the slightest, inform me immediately."

"I thought you would be wanting to oversee things yourself," the Sub-Commander said, a little surprised that Ikari wasn't going to look after this personally.

"I need to formulate an explanation that I can sell to the Committee," Gendo answered, his mind already working on the problem. "Their only concern will be the viability of Unit 01 and how the current situation will affect the Instrumentality Project. I must confer with Dr. Akagi about Unit 01's status before I meet with them."

"As we both know, SEELE will already know about what has happened before you tell them," Fuyutsuki reminded him.

"Indeed." The Commander stood to leave, reflexively pushing his glasses back into place. "Increase the security around Yui. I doubt that SEELE would attempt to do anything to her, but we must take every precaution."

As Ikari left the office, Fuyutsuki could only shake his head in disgust. "Not even a word of concern about your own son or Major Katsuragi."

Fuyutsuki used the walk to the medical facility as an opportunity to reflect on his affiliation with Gendo Ikari. When he had initially joined him in this mad scheme it had been out of fear of death. He had threatened to expose SEELE and the cover up of Second Impact and Gendo had made it very clear that such actions would most likely cost him his life. At the time Fuyutsuki didn't care, and he didn't particularly care for Gendo either, but he had allowed himself to be swayed.

As it turned out he really hadn't been brave enough to sacrifice his life for the truth and the scientist in him had been enthralled by all that NERV's predecessor, Gehirn, and Project E were. The scientist in him had sunk its teeth into the project and all that it entailed and it had ensured that he would be forever caught in Gendo's web. Over time, he had buried his conscience and accepted what he had chosen. They were all going to die in the end and there would be no one left to damn him for his participation in this madness.

He had even gone along with Gendo's plans for his own version of Instrumentality. He sometimes wondered why he had done so because the only person who was to derive any true benefit from it would be Gendo himself. He supposed it was just his own weakness that made him go along with it, after all, he had already sold his soul to the devil that was Gendo when he agreed to join up, thus ignoring his principles and morality in the process.

He couldn't help but wonder what Yui's reaction would be to everything that they had done. She had allowed herself to be taken into Unit 01 in order to protect her son's future, which could only be done by defeating the Angels. He wondered if she had done it to thwart SEELE from attaining their true goal of becoming god, despite the words they spoke otherwise of engaging in this to rid mankind of its suffering. She had never openly shown much in the way of opposition to their plans, but he felt that she had never been entirely behind the idea either. At least, she had not been as zealous about it as their masters at SEELE seemed to be and she may have had a somewhat different view on how and what Instrumentality was and how it should work. Maybe she was just more focused on her work in creating the Evangelion.

The fact that Gendo had abandoned Shinji and was working towards Third Impact himself, although for a different reason, wouldn't sit well with her. She would be horrified by it. He knew that she had loved her son more than anything else and she had hoped that he would grow into a strong, confident young man. What Gendo had done to Shinji, from his abandonment on through everything that had happened since he had summoned the boy to NERV, was unpardonable. Fuyutsuki doubted his participation in that scheme would be received any better by her and it made him feel even more ashamed of the submissive role he had taken in it all.

He had been very fond of Yui when he took her on as a research assistant, and while he had no illusions of ever being lucky enough to form a more intimate relationship with her, he had still been appalled and more than a little hurt and jealous when she told him that she was seeing Gendo. He had known from the start that the man was nothing but trouble.

He knew that her return was going to cast some wide ripples across the proverbial pond. None of the pivotal players in this apocalyptic game would be left untouched by her reappearance. Much of what Gendo had done, the lives he had impacted, was all for his goal of reuniting with Yui. A lot of people had been used and abused in the course of his scenario and some of those people would be scarred for life. He thought of the pilots and Dr. Akagi specifically in that regard. He also knew that SEELE would be all over this. They were on the edge with the old men as it was, but if anything else happened that they thought might put their plans in jeopardy there would be some serious trouble coming their way and he wasn't sure if they would be able to keep them at bay for long.

The former professor shook his head to clear the negative thoughts. What had already been done was done and there was nothing he could do now that would change any of it. Like Gendo, he had made his bed and now he was going to have to lay in it. As for SEELE, they would just have to find a way to deal with them.

The more immediate concern was that even though Yui was back and no matter what Gendo was planning to do they still had Angels to defeat. As much as he wanted to place his trust in the abilities of pilots Ayanami and Soryu, he knew that their best chances for survival were and had always been in the gigantic hands of Unit 01 and its reluctant pilot. But now, all bets were off. Even if Shinji would still pilot the Eva they had no idea if it would still operate now that the soul within it was no longer Yui's but Katsuragi's. Was the Major's soul even still alive inside the beast, and if it was would she be able to connect with Shinji like Yui had?

They would never know until Shinji tried to sync with it again and deep down he knew that the boy would try. He knew that as scared as Shinji was he had a great affection for his guardian and he would want to try for her sake if nothing else. He also knew that if her soul was indeed still alive within Unit 01 Misato Katsuragi would refuse to give up the fight against the Angels and she would fight to the bitter end to protect her pilot. With Unit's 00 and 02 still under repair, they would need to know soon.

"With a little luck we may all come out of this alive yet," he muttered. He sincerely hoped so.

* * *

 _ **NERV Medical**_

Rei Ayanami was in a state of turmoil and confusion, which was a very uncomfortable situation for the girl since she liked things to be plain, simple, and orderly. She was sitting on a bench outside of the protected hospital ward where Shinji and his mother were being kept and even her security clearance was not enough to allow her entry.

On one hand she found herself to be uncommonly pleased that Ikari had been successfully rescued from his Eva. It was what she had wanted after all. However, she felt a great sense of trepidation and foreboding at the appearance of Yui Ikari. Her life, her entire existence, had been created for the sole purpose of reuniting the Commander with his wife in a Third Impact scenario. Now that she had returned from the Eva's core, that scenario was no longer necessary and Rei feared that now, neither was she.

She may still be of some use as long as there were still Angels to be defeated, but what would become of her then? When the Angels were no more would her existence be terminated? Would she be taken into the dark recesses of Terminal Dogma and put down like an unwanted stray dog? All of the resolve and desires of what she wanted for herself as she begged Unit 01 to give Shinji back had now evaporated.

"I…do not wish to die."

She spoke so quietly that even she could barely hear her own voice. But what reason was there for her to be allowed to continue living? Soon, any usefulness that she still had to both NERV and the Commander would be at an end and she would have nothing left.

Her whole life had been structured, charted, and scheduled down to almost the last second of each day. She had no other interests outside of NERV, she had never needed any because the Commander had said it was unnecessary. She had no interaction on a social basis with others because, again, the Commander had said it was unimportant and would only distract her from her purpose. He may have told her that these things were unnecessary and unimportant, but that didn't mean that she hadn't felt a sense of isolation or hadn't heard the unkind words from those around her. Just because she gave no outward reaction it didn't mean that it hadn't pained her to even some small degree. She had simply been able to outwardly ignore it and remain the cold, emotionless puppet she was designed, conditioned, and medicated to be.

She knew full well what the medications she was required to take did to her both physically and mentally. She had been conditioned to be nearly emotionless and it had begun almost from the very moment she took her first breath. Every word spoken to her by Commander Ikari was her absolute and she had been made well aware of the consequences of disobedience and deviation. It wasn't brainwashing because there was no previously learned behaviour or thought process to subvert and change. She began as a blank slate that knew no other way and was shaped and crafted to be exactly what the Commander desired.

The mood levellers she was required to take were insurance should what little interaction she had with others cause her to waver, or even worse, evolve in her behaviour beyond required limits. They altered her moods and deadened her emotional sensitivity. More accurately they made her simply not care about whatever she was feeling. It also made her not care that she was even taking the medications. Thus far nearly all of her emotional reactions barely registered and until now had caused her little in the way of distress. The one exception to that always seemed to involve Shinji Ikari. Despite the drugs and the conditioning he seemed to be able to get through that barrier and make her feel something.

She also took medications to keep her S2 organ from being fully functional. They didn't stop its effects entirely but slowed it greatly. Enough so that it had taken ever since this second version of herself was activated to alter the human components of her DNA and mutate it to match her Angel DNA. When injured she healed more quickly, but not a fast as she could if her S2 was not constrained. Between that particular drug and the physical effects of the others, it made her feel almost numb and at times like it wasn't even real, that it and her soul weren't properly connected.

Other than to the scenario, she had no place to truly belong. She did not have a family in any sense of the word. At one time she had thought of the Commander as her family but she knew deep down that he did not care about her, only what she meant to his scenario. She was his useful tool, a means to an end with no other purpose for being. She doubted that her feelings about Shinji would even be considered in the matter. She had been created to bring the end of the world after all, not to be a normal girl with all of the things entailed in having a normal life. She had been created not to be loved and cared for, but to be used and thrown away. She was disposable.

And what of Yui Ikari? What would she think of the _thing_ her husband had created as a conduit to reunite himself with her? Would she be repulsed by her and consider her a freak like so many others had throughout her young life? Would she desire to see her disappear?

"I am unwanted and unloved," she whispered. "I have no purpose or reason left to exist. I am no longer relevant."

She suddenly became aware of the cascade of hot tears that had began to stream down her face. A sickening, clenching feeling welled up in her chest and she felt like she might throw up. She was not used to feeling such turmoil, she had never before felt such inner pain. Having virtually no experience with such strong emotions she was left feeling helpless and overwhelmed. She didn't know what else to do, so she simply sat there, alone like she always was, and let her tears flow.

* * *

 _ **Misato's Apartment**_

Asuka Langley Soryu, pilot _par excellence_ of the giant red beast known as Evangelion Unit 02, sat on the couch idly flipping through the TV channels, the remote clenched tightly in her right hand. Her face remained virtually expressionless but her mind was churning like a cauldron on full boil. He had done it to her again. The great and wonderful Invincible Shinji had saved the day once again when poor, fragile, helpless little Asuka was getting her pretty little ass handed to her.

She had looked like a complete fool, standing helpless in the Geo-front for all of NERV to see, her beloved Eva missing its arms and its head. Even that fucking doll Rei had put up a better fight. She still couldn't shake the image of Unit 00, seen on footage of the battle after she had been rescued from her damaged Eva, one arm still not regenerated from the previous battle and charging the Angel with an N2 bomb tucked under its good arm. It pissed her off to no end. She wanted to bury her fist in that bitch's face and leave her bleeding on the ground. She didn't want and she sure as hell didn't need Wondergirl's help.

She had shown nothing but scorn when Shinji was absorbed by his berserk Eva, even going so far as to place the blame squarely on him for his predicament. As far as anyone at NERV knew she hadn't been around when the last attempt had been made to free him and if she had her way no one ever would know. It wasn't like she cared what happened to that perverted idiot anyway. Or to Misato for that matter, she could fend for herself just fine. And with her out of the way, Kaji would be hers for the taking.

But she had been there and she saw what happened and she could just picture the scene at NERV. The full attention of the medical staff and all of the powers that be would be gathered around their beloved and prized idiot, making sure that he was whole and fit and ready to resume the fight. They would be falling all over themselves to help their great hero, focusing the attention of the entire organization on a useless, untrained, bumbling fool.

If he wasn't trying to run away, then he was always getting hurt. He was as unreliable as he was useless. They should be throwing their resources behind her, not him. She was the best pilot, she had the best training and an Eva that had been truly built to fight the Angels, not some test model or prototype like the idiot or the doll piloted. She would show them all how it should be done and maybe then she would finally get the recognition she should have been receiving all along.

' _He just wants to be your friend. That's all he has ever wanted. He want's your friendship and he wants to help you,'_ a voice in her head told her. She had been hearing the voice a lot lately and she didn't like it one bit.

"I don't need that pervert's friendship or his help," she snapped. "He's useless and he's a coward!"

' _But he helped you defeat the Sixth,'_

"He was in the way!" she growled. "He ruined my first battle and he stole my glory!"

' _He was so patient with you and trained so hard to beat the Seventh.'_

"He was the one who kept screwing it up!"

' _Rei synchronized with him in one try.'_

"Fuck you and fuck Wondergirl! She's a lifeless doll! She's nothing!"

' _He disregarded his own safety to save you in the volcano.'_

"I'd rather die a warrior's death than be saved by that idiot!"

' _You goaded him into taking the lead against the Twelfth.'_

"It was his fault for trying to show me up! He got what he deserved!"

' _You wanted Misato to punish him for being reckless.'_

"She said she would! She would have punished me for the same thing but she throws herself on him and cries like her lost love has returned." She threw the remote across the room. "First she takes Kaji, now she wants the baka!"

' _You kissed him.'_

"I was bored and he sucked at it! Misato can have him! They can do all of the perverted things they want to each other. I. Don't. Care!"

' _He saved you again from the Fourteenth.'_

"After he quit!"

' _But he came back and he paid the price.'_

"If he wasn't so incompetent his Eva wouldn't keep going berserk!"

' _His mother protects him.'_

The knowledge that his mother had been within the Eva's core had brought implications to her mind that she didn't want to address and she had been avoiding thinking about it ever since she left headquarters. It was just more explosive fuel to be set off by the lit match of that annoying little voice in her head.

She flew off the couch in a screaming rage, knocking over the furniture and throwing anything she could get her hands on across the apartment. She called Shinji a useless, perverted idiot and called Misato a slovenly, drunken whore in three different languages. She called them every filthy name she could think of, insulted everything about them, and screamed how much she hated them.

' _His mother protects him.'_

She fell to the floor, her fists jammed tightly to her temples, her head feeling like it was exploding.

"Shut up! Shut up! Shut up! Why does he get to have his mother back?! Why him?! Why is everything always for Shinji?!"

And that, for Asuka, was the root of the matter.

* * *

 _ **Central Dogma**_

Ritsuko Akagi stood on a catwalk within Central Dogma, leaning on the handrail and looking down at Unit 01. Her world had just been turned upside down and inside out all at the same time. Technicians both down below and in the command centre were busy taking readings and re-calibrating equipment. In front of the Eva's core, a wide area had been cordoned off with yellow caution tape. No one was to approach it until every possible scan and reading had been taken and analyzed. Misato and Shinji's clothes were the only things within the marked off area.

Ritsuko found that she couldn't get the image of her friend's absorption out of her head. True, their relationship had been strained lately, but Misato was still her closest friend. She knew Misato was a messed up individual, who wouldn't be after witnessing Second Impact first hand, but one of the things she admired most about her purple haired friend was her ability to let her emotions show and to hell with who didn't like it. Misato's emotions were always lurking just under the surface and were easily coaxed out, while she on the other hand tended to suppress hers to a large degree.

It was so like Misato to be as upset as she was over what happened to Shinji. After all, he wasn't just her responsibility, he was family to her. It wasn't even all that surprising when she started screaming at the Evangelion and beating on its core with her fists. That was Misato Katsuragi in a nutshell. When all other options failed, she would fight, even if it meant a bare knuckles brawl against an Evangelion. Ritsuko couldn't say if she would have reacted that way if she was in Misato's place and that disturbed her a great deal. She didn't have anything in her life that she was willing to fight that hard for.

All of her life, all she had really cared about was her science, never really becoming emotionally attached to anyone or anything. Except her cats and she realized that for what it was. She had a lot in common with them, they were emotionally detached and indifferent to most of the world around them. They were her crutch, something to identify with. She let out a disgusted sigh. _'Pathetic! I have more in common with my cats than I do with other human beings.'_

She hadn't fared well socially early in her life and she had been a disaster in the dating department, all of which had served to lead her deeper into her studies. It had also been one of the biggest catalysts that led her into the uncaring arms of Gendo Ikari. He had the type of personality that seemed to draw in the weak and vulnerable and demanded them to do his bidding. Even when she first realized that he didn't love her and was just using her, sometimes roughly, she couldn't walk away. Their physical relationship was the method by which he bound her to his will. She was desperate for human contact, any kind of contact, and she needed to feel loved. She didn't get that from him, but she still couldn't seem to walk away. So she settled for an illusion of love and made believe that it was real when all she really was to him was his whore.

Career wise, she had everything she could possibly want and more. She was on the cutting edge of science and technology here with NERV. Bio-mechanical technology, genetics, cloning and soul transference, the MAGI system. Any scientist in the world would sell their soul twice over to be involved with the technologies she had her hands on every day and it did give her a certain sense of superiority. A sense that she was important and worth something. A sense that was always crushed whenever she was with Gendo. Whether it was within the NERV complex or in his bed, the dominance of his personality seemed to crush her will and, over time, it had crushed her spirit as well.

And now Gendo had Yui back and in a way much better than his scenario ever could have realized. Ritsuko knew that it was the end of the line for her one sided relationship with the Commander and even though it was very hard for her to admit it, it was probably a good thing. Maybe the best thing that could happen to her. She was starting to realize some things about herself, she was seeing things happen to her personality that she really didn't like very much.

It was a rare instance of self reflection that actually surprised her but she realized that she was at a crossroads and had to make some decisions. She could either continue on as she was, thus risking what she considered to be her already questionable sanity, or she could try to move in another direction and hopefully find something that was tangible and real. Unlike her mother had, she felt no ill will towards Yui Ikari, though for a time she did resent her since she was Gendo's obsession and the only thing he truly loved. When she began to realize that she really was nothing but his tool she got over it. She had never actually met the woman and knew nothing of her other than her scientific reputation, which was considerable. However, since she saw the woman emerge from Unit 01's core she had felt a certain amount of fear.

She had no idea how much of the outside world Yui had been aware of. Was she aware of Gendo's plans and what role she had played in them? Did she have an inkling of all of the awful things that had been done? Would Yui even want anything to do with the Commander after all he had done, especially when he had abandoned and used his own son? How would she react to her, the pathetic excuse of a woman who was having sex with her husband while he schemed to reunite with her soul at the cost of the entire human race? Someone, who for all of her brilliance, was too damned stupid to get away from a man who was only using her?

"I've got a lot to answer for no matter who's asking the questions," she said quietly. "I'm such a damned fool and I'm so sick of myself. I can't live like this anymore." She offered a wistful smile to the purple behemoth before her. "I could really use your help right now Misato, and what do you do, you go and get yourself absorbed into an Eva."

She felt a vibration on the catwalk and turned to her left to see the Commander approaching her. She suddenly realized just how truly tired she really was.

"Commander," she greeted him, not bothering to move from her position, leaning on the rail.

"Doctor," he returned. "Status report."

"We're still working on our sensors and going over the readings we obtained from the event."

"I will need more than that to take to the Committee, Doctor. They will want a report on what happened, how it happened, and the viability of Unit 01."

"I'm well aware of that," she replied irritably. "Until we finish analyzing the data we won't know how or why, and we may not then. As for Unit 01's viability, that depends on whether or not Misato's soul survived the transfer. If it did, we won't know if Unit 01 will operate until we try. In order to do that we will need Shinji to try syncing with it."

"Unit 01's pilot will be made available as soon as he has been cleared from the isolation ward," he informed her coldly. "In the meantime I expect all possible measures to be taken to investigate this incident and to look into Unit 01's continued ability to operate. Are we clear on this Doctor Akagi?"

"Yes Commander, we are," she answered, barely able to control her anger. _'Unit 01's pilot? He couldn't even refer to his own son by his name, and he couldn't care less that Misato is stuck inside the core!'_

"Then I expect results soon," he said as he turned to leave. "You do realize Doctor Akagi, that our private relationship is at an end." He didn't even look at her when he said it.

"Yes, I managed to figure that out all by myself," she snapped.

He simply walked away from her without another word. For her part, Ritsuko felt the sudden need to throw up.

* * *

Please leave a review if you would be so kind.

And while you're here, check out my other stories.


	3. Chapter 3

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

 **Transposed**

 _ **Chapter 3**_

 _ **Inside Unit 01's Core**_

Misato Katsuragi slowly returned to something resembling consciousness but found herself encased in a fog of confusion. She felt very strange, she didn't know where she was and she couldn't see much of anything in the reddish gloom that surrounded her. A feeling of panic began to set in before her mind finally started to piece things together.

' _You can't have him! I won't let you have him!'_

The memory flashed across her mind. She remembered crying, crying because Shinji was lost within Unit 01's core. She had started beating on the core with her fists.

' _Give him back! Give me back my Shinji!'_

Something seemed to envelop her, physically and mentally, and pulled her into the Eva. She was in shock as her brain registered what had happened to her.

"Oh God," she gasped in horrified realization. "I'm inside the Eva." She felt the panic begin to creep back in on her and she very nearly gave into it. Panicking was probably the worst thing she could do right now and it took a major effort to convince herself to calm down. Eventually, even the disoriented feeling she had from before faded away.

She let her mind go back over the sequence of events again, hoping to pick up anything else she hadn't remembered yet. She had been hysterical when she started battering the core and at the moment she was absorbed she seemed to freeze and had the strangest sensation, like she was being separated from her body. Something that was ungodly powerful and frightening, yet somehow soothing at the same time had caressed her mind. The sensation was fleeting and seemed to go away as quickly as it had come.

She had felt something pass by her as she was brought fully into the core. _'Shinji,'_ she thought. _'He was on the way out.'_ She then remembered seeing another form not far behind him. It was the form of a pretty young woman who looked to be about the same age as herself. She remembered touching it and a feeling like an intense electric shock went through her. The first thing that came to her was an identity.

Yui Ikari.

She had found herself awash in other memories. The same young woman in a maternity ward, giving birth to a healthy baby boy. The same woman waving to her happy and laughing child as she entered the entry plug of Unit 01. The sense of intense sadness and longing as she allowed the beast to take her within itself for the sake of her child's future.

In a heartbeat, and without hesitation, Misato Katsuragi had committed the most selfless act of her entire life. She had grabbed the form of Yui Ikari and pushed it in the direction Shinji had gone.

' _You belong with your son.'_

As the woman disappeared from sight, other memories from her life, as well as her time within the Eva flashed through Misato's mind in a disjointed collage that had eventually rendered her unconscious.

"So here I am, in the belly of the beast," she thought. "Now what?"

Her mind once again settled on some of the images that had gone through it before. Images of Yui within Unit 01.

"Maybe if I can sort through those memories I can get some idea of what I need to do in here."

She didn't know if she could make sense of any of it or not, or if it would even be helpful, but she had to occupy herself with something or she would go mad. Truth be known, she felt very much alone and she was very, very scared.

* * *

 _ **NERV Medical**_

Yui Ikari awoke slowly, a strange feeling instantly apparent to her senses. No, not so much a strange feeling really, more like a long forgotten one. It had been a long time since her soul had resided within a physical body. She opened her eyes and instantly closed them again, the light being too harsh. She opened them again, slowly this time, allowing them to get used to the light. As her vision settled on the plain white of the tiled ceiling, her conscious mind confirmed her began to remember.

The voices of two women. One quiet and pleading with the beast, the other a voice filled with a great deal of pain and grief, calling out to her son, telling the Eva that it couldn't have him, that she wouldn't let it have him. She felt the pounding on the core as her Shinji drifted towards the voice, making his choice to go back to the outside world.

She had shared her son's memories while he was within the core, just as she did whenever he synced with the Eva, so she knew that the voice belonged to the woman who had been kind enough to take him in. The only one to show him any care and concern since _he_ had summoned him. It had surprised her when Major Katsuragi was pulled into the core and before she could react to it, the two of them touched, sharing each others memories and Misato pushed her after Shinji.

' _You belong with your son.'_

"Yes, I do," she whispered to herself. "It's where I should have been all along. I was foolish to leave him in the first place, I realize that now. But the price you're paying to rectify my mistake is too high Major Katsuragi." That woman had already been through enough in her life, she had seen that in her memories with startling clarity.

She massaged her temples briefly, an annoying buzz coming and going in her head and making her feel like she was forgetting something. Whatever it was, if it was anything, it would come to her in time she was sure. She turned her head to the left and saw her son sleeping soundly. They were separated from each other by a glass wall. They were obviously in quarantine.

She smiled sadly. "I'm so sorry Shinji," she said softly. "If I had thought for a moment that he would abandon you, I never would have left you."

The main door to the isolation suites opened and she saw the figure of her old professor enter the room. He walked up to her cubicle, his gait almost hesitant, and pressed the button on the intercom.

"I'm glad to see you're finally awake," he greeted, trying to keep the nervousness off of his face.

"It's good to see you again Professor," she said, genuinely glad to see her old teacher again.

"I have been put in charge of overseeing your care," he told her. "How are you feeling?"  
"A little tired and weak, but otherwise fine." She looked to her son. "What about Shinji?"

"All indications point to a case of exhaustion," he assured her. "He will be fine. But, I'm afraid neither of you will be able to leave until they've run every test they can think of."

" _His_ order's I suppose," she said with a hint of venom in her voice. Fuyutsuki didn't fail to notice it.

"I'm afraid so." He paused for a moment, gathering his thoughts. "How much of the outside world were you aware of Yui?" It was a question that he didn't want to ask, not now, but he had to know.

"I was as aware as any other creature, even when the Eva was shut down," she answered. "If you're asking how much I know of what has been going on, I can tell you that I know enough to tell that I don't like it. We need to talk Professor. Before I talk to Gendo, I want to know exactly what has been going on. I think I deserve that much."

"That may be difficult to arrange without being monitored," Fuyutsuki told her, his face grim. "But I will try. I have initiated a loop in the monitoring program for this room, so I only have a few minutes to speak freely before regular monitoring resumes." He paused again for a moment. "Suffice it to say that after some much needed and long delayed self reflection, I have decided that I don't like what I have become, or what I have been a party to. I fear it is too little and too late coming and I can't expect you to forgive me, but I will try to make amends. I will tell you everything I know as soon as we have a chance to do so, free of the eyes and ears of others."

"I want Shinji to know as well," she told him.

"That may prove to be too much for him," he cautioned. "Are you sure?"

"He needs to know and I will be here to get him through it. They all deserve to know. What about Major Katsuragi?" she asked, her concern genuine.

"We don't know yet," he answered sadly. "Dr. Akagi is still going over the data and they need to re-calibrate all of their monitoring equipment before they begin scanning Unit 01 again."

"I'm sure that she is all right," Yui told him with a sad smile. "She pushed me out of the core you know. She said I belonged with my son."

"So she sacrificed herself so that Shinji could have his mother back," he speculated. "If it comes down to it, I'm sure that she will protect him just as fiercely as you did Yui."

"It will come down to that," she told him. "We both know that. Remember, I've seen the scrolls as well so I know what's coming. That's why I built the Eva and became one with it. And I have no doubt that Shinji will be able to sync with her. They have very strong feelings towards each other and I know that she will protect him."

"Hmmm," he thought, allowing a slight smile. "I'm not sure I want to see Unit 01 go berserk with Major Katsuragi as its soul." He checked his watch. "The monitoring is about to start up again. We'll talk later."

"Yes, we will," she assured him. She smiled warmly at him. "It really is good to see you again Professor. You, I think I may be able to forgive. Him…I don't think I can."

He was visibly relieved. A chance of her forgiveness was better than none. "Thank you Yui, and I'm glad that you're back. I'll try to have them get these tests finished as quickly as possible and get both of you into a normal room."

"Please do," she said, once again looking over at Shinji. "I want to hold my son again."

* * *

 _ **Office of Gendo Ikari**_

A single holographic display provided most of the light currently illuminating the Commander's office. He had lucked out in having Chairman Kiel be the only one to meet with him, or at least be the only one to make his presence known. Kiel was always level headed whereas the other members of SEELE often tended towards irrational outbursts and rampant paranoia, and while he could take advantage of that from time to time, this was not an instance where he wanted to be exposed to it.

"A most interesting and unexpected development Ikari," Kiel said after hearing the details of the incident. "And a troubling one as well. This endangers the scenario greatly."

"It is too early to make that conclusion," Gendo told him. "We are in the process of investigating Unit 01's viability. If Major Katsuragi's soul has survived the transfer I have every confidence that Unit 01 will remain operational."

"And what do you base this on?"

"She has a great deal of affection for the pilot of Unit 01 and has become like family to him. Without a doubt she will accept him when he tries to sync with the Evangelion," Gendo explained, his hands never leaving their usual spot in front of his face. "She also has a great deal of hatred toward the Angels and will not hesitate to do what it takes to destroy them."

"We need all options in our hands Ikari, we cannot afford to lose Unit 01," Kiel reminded him. "If she goes too far to destroy an Angel and is herself destroyed, it will jeopardize the goals of the Project."

"Her connection to the pilot will prevent her from going too far," he assured Kiel. "She will not allow him to suffer any undue harm, thus she will not destroy Unit 01 in the process."

"You are banking everything on this woman's soul even being capable of synchronization in the first place. Not to mention that she is not as stable an individual as the previous soul to inhabit Unit 01's core."

"That is an unavoidable consequence. If not for Major Katsuragi's presence we do not believe that the pilot would have been retrieved at all. As you are well aware Unit 01 would not have accepted another pilot nor the dummy plug system and would have been useless," Gendo reminded him.

"It may well be useless now," Kiel retorted. "You are on very thin ice Ikari, you had better have something far more substantial to report when we meet next time or there will be consequences." With that the hologram disappeared.

Gendo remained motionless for several minutes, ordering his thoughts. "What do you think Fuyutsuki?" he asked.

The Sub-Commander stepped from the shadows. "It could have been a lot worse."

"We need to determine if Unit 01 is still viable and we need to know soon," Gendo reminded him. "But the only way to do that is to perform a sync test with the pilot."

"Shinji," Fuyutsuki made a point to specifically call him by name, since Gendo seemed to have forgotten it. "Is suffering from exhaustion and it would not be wise to attempt a sync test until he has had some time to recuperate. And I just saw Dr. Akagi, she looks like she is ready to collapse. If we are to expect any kind of positive result we need our personnel to be capable of performing their duties."

"I suppose you are correct," Gendo grudgingly admitted. "But we cannot afford to wait for long. Take whatever steps you feel are necessary but keep in mind that we are extremely limited in how long we can put this off."

"I understand," the older man said as he turned to attend to it.

"Fuyutsuki," Gendo called, his voice taking on a softer tone.

"Yes Commander?"

Gendo maintained his usual posture. "How is she?"

"A little weak and tired, but otherwise fine."

"She is not going to forgive me, is she?"

Fuyutsuki may not have been Gendo's biggest fan, but he wasn't going to lie to him on this. "I don't think so, no."

Gendo was silent for a moment. "She is alive and back in the physical world, that is enough."

' _For now.'_

* * *

 _ **NERV Medical**_

Shinji Ikari slowly opened his eyes and was greeted by an all too familiar sight, the ceiling of a hospital room. He wasn't surprised really since it was an all too common and seemingly inevitable occurrence for him whenever he piloted. His mind felt kind of fuzzy, like he had been asleep for a very long time and was slow to wake up and he was having a bit of trouble ordering his thoughts. He was tired and his sluggish mind was having a hard time recalling the details of just exactly how he ended up here.

"Shinji," he heard a soft, female voice call. There was a familiarity to it that touched something deep within his mind. He rolled his head to the right and was met by the anxious and smiling face of a pretty woman with brown eyes and brown hair, who was sitting in a chair next to his bed. He was confused until his brain decided to catch up to the input it was receiving from his eyes. Half remembered images of his last battle and its aftermath came into his mind. He couldn't recall much after Unit 01 went berserk, but other images flashed in his mind. Images of the woman sitting next to him teased his brain until he could put them together.

"Do you remember me?" she asked hopefully.

"M...mom?"

Her smile got wider and a tear rolled down her cheek. "Yes Shinji, it's Mom."

He didn't know if he should believe it. He had been barely able to remember his mother. The last time he saw her before she died was a memory that he could hardly recall since he had been so young at the time. He wanted to believe it more than anything in the world, but it couldn't be true could it? He had never understood what had happened to her, he only knew that she was gone. His father had never explained to him what happened that day, hadn't even kept any pictures of her. Shinji always wished that he had at least that much to remember her by but he wasn't even allowed that small measure of compassion from his father. Was it really her, was this really his mother?

In the end he went with what his gut and his heart were telling him and what he hoped beyond all reason to be true. With all of the energy he could summon he sat up and launched himself into her embrace.

"Is it really you Mom?"

"It's really me Shinji," she cried happily. It felt so good to be able to hold her little boy again.

"I'm afraid I'll wake up and this will have just been a dream," he cried. "I've missed you so much."

"It's not a dream Shinji, I'm really here and I'm not going to leave you again. I promise."

They cried in each others embrace until the flood of emotions and his exhaustion took over and Shinji was soon asleep again. Yui contentedly curled up on the bed with her son in her arms and quickly fell asleep herself.

* * *

 _ **Eva Cages, Central Dogma. The Next Morning**_

Asuka was a mess. She was exhausted and her pride driven facade was cracking and falling apart. She hadn't slept a wink all night, her mind in too much turmoil to allow her to rest. When it had become obvious that there was no use in trying anymore she had showered and dressed in her school uniform, though she doubted she would actually make it to school today, and headed for NERV.

Two things had been vying for dominance within her head. The first was the idea that something of her mother may reside within Unit 02. The very concept of such a thing had shaken her to her core. She had to know, but at the same time she was deathly terrified to find out. She wanted it to be true, she wanted it more than anything she could ever possibly imagine. She wanted to know that her mother was still with her, but she had seen what was left of her mother's mind up until the time she killed herself and she was afraid of what part of her may be left in Unit 02.

She had loved her mother so much and her insanity and suicide had devastated her, turning her into the over driven young girl she had become. She had thrown away her childhood at that point, running away into adulthood far too early. She had thought that if she ran far enough she wouldn't be able to hear her mother talk to a doll as if it was her. Maybe she could run far enough that she could no longer see her mother hanging from the ceiling, a memory she had been trying to keep at bay all night without a great deal of success.

The cold and hard truth was that she could never run fast enough or far enough to get away from it and she knew it. Seeing Shinji's mother appear out of Unit 01's core had let it all catch back up to her. She wanted to blame Shinji for that too. She couldn't help but wonder if he had ever felt anything of his mother's presence inside Unit 01. Did he know that his mom was there? Was that why he seemed to feel safe and comfortable in Unit 01's entry plug? Was he ever able to communicate with her?

The other thing on her mind was Shinji himself. She was of two minds about him really, as if there were two Asuka's. Well, in a way there was. There was the tough, confident, loud, and rude Asuka that she showed to the world. Then there was the scared and lonely Asuka, the true Asuka that she refused to let anyone see.

The rude Asuka thought of Shinji as being nothing more than a spineless, perverted idiot who was scared of anything and everything, including his own shadow. A pathetic moron who somehow beat her sync scores and managed to pilot his Eva to victory after victory, most of the time nearly getting himself killed in the process. The Shinji who was everything she hated. He was lucky, something in the infinite reaches of the cosmos obviously had a soft spot for fools like him.

The soft Asuka though, the source of that annoying voice she had been hearing so much lately, the part of her that was imprisoned behind the barriers she had erected, saw someone who was a lot like her. Afraid and alone in the world, a person who measured their worth to the rest of the world by their ability to pilot the Evangelion. Someone who just wanted to feel needed and loved. The soft Asuka understood Shinji. She understood why he was lonely and scared and always apologizing for things that were beyond his control. She wanted to tell him how she felt, wanted to feel his embrace and know that someone was there for her, that they could be there for each other.

She knew that he liked her, although she wasn't sure how much, despite all of the things rude Asuka had done to him. She liked him too and really did want to be his friend. Anything beyond that she wasn't sure of. She wished she was strong enough to open her heart to him and let him in, but she wasn't. That was the weakest thing about her. Besides, the rude Asuka was the one in the driver's seat right now and she didn't seem to want to hand over the keys and relinquish the steering wheel any time soon. Stubborn bitch.

Before she realized it, she found herself standing on the umbilical bridge in front of Unit 02. Her Eva should soon be ready for duty once again if the repair schedule she had seen was correct.

"Are you really in there Mama?" she asked quietly. "Have you been with me all along, like Shinji's mom has been with him?"

"It might be easier to get that answer if you ask the next time you sync."

Asuka whirled around to see Dr. Akagi standing behind her. She was going to issue a sharp rebuke until she got a good look at the fake blonde. Her clothes, lab coat included, were rumpled an unkempt, her hair was a mess, and her severely bloodshot eyes had dark circles beneath them. Something sad had settled within those eyes.

"Mein Gott!" she exclaimed. "You look like the walking dead!" She suppressed a far angrier retort, knowing that the reason Akagi looked so bad was due to her efforts to retrieve the invaluable baka from his Eva. However, she needed answers right now more than she needed to harangue the exhausted scientist.

"Thanks ever so much. I haven't slept in three days," Akagi said, her voice slurred from fatigue. "Been living on bad coffee, cigarettes, and whatever junk food is within reach."

"Did you know that Shinji's mother was in Unit 01?"

"Right to the point I see," Akagi observed as she sipped on her latest cup of evil brew. "Yes, I knew."

"So is my mother in there?" Asuka asked her, pointing at Unit 02.

Ritsuko was so sick of the secrets and she was so tired she didn't even have the energy to lie. She just couldn't do it anymore. Her soul couldn't bear the weight of it any longer.

"Yes, your mother's soul, or at least whatever part of it that remains, is inside Unit 02's core."

"I see," the redhead said quietly, thinking for a moment. "Hypothetically speaking, could you get her out like you did with Shinji and his mom?"

"Our procedure didn't release Shinji," Ritsuko answered. "It should have, but I don't think Shinji wanted to come out."

"Then how did they get out?" Asuka asked, puzzled, her voice taking on a hard edge.

"I think Misato's grief lured him out," the doctor answered. "As far as why his mother came out too, we don't know yet and I don't know if we ever will. And before you ask, we don't know if Misato's still alive in there."

"If she is, will Unit 01 still operate?"

"We won't know the answer to that until Shinji tries to sync with it."

"So how is the baka anyway?" Asuka asked, sounding very much like she didn't care. Fortunately, the voice in her head remained quiet.

"I have no idea," Ritsuko answered with a trace of bitterness. "Even I wasn't allowed into their ward. Evidently my involvement wasn't required. Why don't you go see him, I heard they've lifted the quarantine on them."

"I'll pass," the redhead answered dryly.

"Suit yourself," she said as she took the last swallow of her coffee. "Don't let him get to far away from you Asuka, you'll regret it later."

"I have no interest in that perverted little dummkopf," she snorted. She clenched her fists so tightly that her fingernails began to lacerate her palms. It was taking every bit of self restraint she could muster to keep herself from beating the fake blonde into a bloody lump of meat.

Ritsuko was so dead tired, she didn't even notice Asuka's agitated demeanour. "Whatever you say. I'll tell the tech crew to leave you alone for a while."

"Thanks," Asuka said curtly before sitting down on the edge of the umbilical bridge in an effort to try talking to her mother.

* * *

Please leave a review if you would be so kind.

And while you're here, check out my other stories.


	4. Chapter 4

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

 **Transposed**

 _ **Chapter 4**_

 _ **Inside Unit 01**_

Misato sat within the core in utter disbelief. She hadn't been able to make much sense of all of the thoughts and images she had acquired from Yui. There was simply too much there and it was moving through her mind at a speed she couldn't handle and she was only able to get a vague outline of things. Heck, it was all she could manage to not collapse into a twitching heap until her own mind could sort itself out.

But the little bit that she had been able to deduce from it all was that Second Impact hadn't been an accident and that there were those who wanted a Third Impact, but of their doing and not the Angels. It had something to do with a belief that man had reached an evolutionary dead end, or something like that. And it seemed that the Commander had some plans of his own. She wasn't sure if her deductions were correct but it was the best she could do at the moment with her mind in the state it was in.

Besides the memory overload, she was just plain scared. Almost as scared as she was upon witnessing Second Impact. She was trapped inside the unpredictable, berserker prone Unit 01, which for all she knew might be an Angel itself, although under NERV's control. Barely. The fact that it had a core like the Angels and that it had regenerated its own freaking arm out of a piece of the Fourteenth, before it started to _eat_ the damn thing, had made her start wondering again just what the hell the Evangelion really was. It was a question that no one had been willing or able to give her an answer to thus far.

She was also still very worried about Shinji. For a month she had worried herself sick about him and now she was still no closer to knowing if he was alright than she was before. She hoped that both he and his mother had made it out alright and were none the worse for the experience. It had put her in a hell of a predicament, but if it meant that Shinji could have his mother back and have even a remote chance of a normal life and being happy, providing they managed to defeat the Angels of course, then she supposed it was worth it. Even if she was now isolated, alone, afraid, and didn't know if she would survive in here, let alone see the outside world again.

She remembered Shinji telling her once that for some strange reason, despite the pain he often had to endure while piloting, he seemed to feel safe and comfortable in the entry plug within Unit 01. She now understood why. It was because his mother was looking after him when he was synced. When Unit 01 moved on its own or went berserk, it was Yui protecting her son. Yui had also protected him from the raw consciousness of the Eva itself. From what Ritsuko had told her while Unit 01 was chowing down on the Fourteenth Angel, and with what little she had been able to pick out about it from Yui's memories, she knew that the Eva was essentially alive and had a certain amount of awareness. How much, she was unclear about, but she was pretty sure that she wasn't going to be able to just take over the beast she now was trapped in without a confrontation of some sort.

She knew that her encounter with that consciousness would be coming soon, instinctively she could all but feel it lurking all around her like a dark shadow, slowly closing in. Had Yui Ikari been able to overcome it because it had somehow seemed to understand her basic, instinctive desire to protect her child? If that were the case then she didn't like her chances. She wasn't a mother and even though she had tried, she knew she had failed miserably at acting anything like a parental figure to Shinji. She wasn't his mother. She cared about him, hell, she did love him in her own way and she would give her life if necessary to protect him. She wondered though if that desire to protect him would be enough.

As she felt the consciousness getting closer she tried to swallow her fear and her doubts and tried to prepare to do what she did best when backed into a corner. Fight. It wasn't that she didn't have confidence in Rei and Asuka, but if she wasn't accepted by Unit 01 then their chances of defeating the Angels was going to be in deep trouble. Not to mention that it might mean the end of her own, tortured existence.

As screwed up as she was, she really wasn't ready to die just quite yet.

* * *

 _ **NERV Medical**_

Yui Ikari had awakened very early, roused from her sleep by nightmares of things she knew and things she could only guess at. Ever since she had spoken to Professor Fuyutsuki she had been running down in her head all of the tidbits of information she knew about what was really going on at NERV. Thankfully, the ability of her scientist's brain to process large and complicated streams of information, and her synchronizations with Shinji as well as Rei and Asuka during cross synchronization tests, had given her plenty of practice at processing the memories of others into coherent information.

Her prior knowledge, along with what she had gained from her contact with Misato and the others had given her a good picture of the situation, but she knew that she didn't have all of the answers yet. Or at least not the confirmation she was seeking to what she knew. If she could do so, she would like to talk to everyone she could at NERV and find out as much as she could before confronting Gendo and hearing his version of things, but she knew that wasn't possible.

She had taken a long, hot shower, enjoying it immensely, before roaming the hallways near the room she shared with her son. Using her own body again was taking a little getting used to and it felt good to stretch her legs. As she slowly walked up and down the halls her mind returned to the unpleasantness of her dreams. There was still much that she didn't know, but she knew more than enough to realize that she had made two very large errors in her life.

The first one was letting herself be absorbed into the Eva. If she had known that Gendo would abandon Shinji afterwards, she never would have done it. If someone had told her at the time that Gendo would have done what he did she wouldn't have believed them. She knew of his past behaviour and of his emotional inadequacies but she never would have thought in a million years that he could have or would have abandoned his own flesh and blood like he had. The other mistake, in retrospect, was marrying Gendo in the first place. Though, she could live with that one because she had Shinji, apparently the only good thing to come of their relationship.

The mere thought, let alone the cold hard fact that Gendo could do something as cold and as heartless as turning his back and walking away from his own son made her furious. She had always thought that when the day came for Shinji to be introduced to the Evangelion and become its pilot, she would see that her son had become a healthy, happy, well adjusted young man. She had missed him terribly and even though her resolve had remained strong while she waited for that day, it had saddened her that she wasn't able to be there to guide him and look after him. To watch him grow and become the fine young man she always hoped he would be.

It had broken her heart that day to see the nervous, timid, and clearly scared to death young boy that had been brought in front of her. She could almost feel the sadness, the loneliness, and the anxiety radiating off of him in waves as he was brought lower and lower by his father's words. Then, after he had torn the boy down as far as he dared at that moment, Gendo had the audacity to have Rei wheeled in, the poor girl half dead, bleeding and in pain, and he used her to play on Shinji's gentle and fragile nature to make him pilot the Eva. Yui came to understand as the weeks went on that every single action Gendo took towards his own son was premeditated and deliberate, designed to place the boy in the fragile frame of mind he wanted him in and keep him there.

When Gendo had used the dummy plug to make Unit 01 destroy the possessed Unit 03 she very nearly went berserk and attacked the manipulative bastard, squashing him like the cockroach he was. She would have if the dummy plug system hadn't somehow interfered with her ability to take over. She learned from it and was able to reject it when he tried to activate it for the battle against the Fourteenth.

She stopped at a bank of windows that looked out over the Geo-front and took some deep breaths to calm herself. She was not someone who was prone to fits of anger, far from it actually, but she was finding that just the mere thought of Gendo now made her angry and sick to her stomach at the same time. There were a lot of things she could imagine forgiving him for but abandoning their son wasn't one of them. Not only had he abandoned Shinji, he had manipulated him like he had done to so many other people. He didn't care who he hurt, or how badly he hurt them, so long as he got what he wanted. One thing she knew for sure was that she wouldn't let him hurt Shinji again.

She should save some of that anger for herself however, since she also knew in all of this that she was a horrible hypocrite. What had she done if not abandon Shinji when she let herself be taken by Unit 01? How stupid, naive, and shortsighted had she been to ever think that the concept of Instrumentality was going to give him a better future, even if the last ten years of Shinji's life had played out the way she hoped and expected?

She'd been plagued throughout her life by a streak of naivete. It had shown itself in her belief that she could be the remedy for what ailed Gendo and it carried on through her belief in the Instrumentality Project and that stupid naivete had all but ruined her son. Why couldn't she see it back then? She was going to make sure Gendo never hurt him again and she'd be just as well served to include herself in that statement. She was just as guilty as Gendo was.

* * *

Unbeknownst to Yui, a certain blue haired, red eyed girl was watching her as she walked the hallway. Rei had stayed at the hospital for several hours after Shinji and his mother had been recovered, her emotional state rendering her almost immobile. It was early in the evening when she was finally able to get to her feet and make her way home. She was emotionally exhausted and didn't quite remember the trip.

When she got to her rundown apartment she had shuffled towards her cramped and rust stained shower, leaving a trail of her clothes across the cracked and stained linoleum as she went. Like usual, the hot water was sporadic but she spent well over an hour just standing under the often cold spray anyway, trying not to think about or feel anything. She enjoyed little success in that regard.

She had not been allowed into the isolation ward to see Shinji and no one would speak to her, not even when she asked about his condition. No one had given her a second glance while she sat in the hall and cried from the depths of her soul, alone and afraid. The Commander had not yet contacted her in regards to her future now that his plans were seemingly no longer necessary. She was useless to him now and apparently he didn't even think enough of her to tell her so.

She had exited the shower, covered in goose bumps and shivering and went to her bed. She didn't sleep, but instead she spent the night backed into the corner at the head of her bed, naked and staring sightlessly across the confines of her decrepit home, almost afraid to close her eyes. At some point the tears came again, but along the way she resolved to go back to the hospital in the morning and see not only Shinji, but his mother as well. She felt a great need to speak to her. She needed to know if the woman who's soul she had been tasked to reunite with her maker during Instrumentality despised her as well, or if she could forgive her for being the pale imitation of a life and the mere tool that she was.

She had been watching Yui for several minutes, trying to harden her wavering resolve to talk to the woman. She had never been good at talking to people, let alone initiating the conversation. It was another of the aspects of life that had been deemed unnecessary for her to experience. It was easy to control someone when they had no outside influences to sway their opinions and behaviour and knew only what their master allowed them to know.

But there was more than her programming by the Commander that was keeping Rei from walking up to her. She was genuinely afraid. Afraid of what Yui Ikari would think of her, though she wasn't sure why because fear was not something she normally felt and she didn't generally give too much thought to what others thought of her. She was afraid of what the woman's return might mean for her future. She was also afraid that her origins would now become known and she would lose her only friend in Shinji.

She felt her resolve leave her completely and she felt more alone now than she ever had before. As the tears threatened to overcome her yet again she turned and silently walked away. Perhaps Soryu was right after all. She really was a doll, unable to do anything without being ordered to do so. Like a marionette, without someone pulling her stings she was unable to function. She had no purpose.

The Commander had given her a purpose, to die on cue like an actor on a stage. Her life was a life without hope. That was something else that had been considered unnecessary because unlike the rest of mankind she knew the purpose for which she had been created and hope, she had been told, was irrelevant. She had believed in the Commander, she had thought that he cared for her but it had become obvious to her that the puppeteer cared little for his puppet. She was just a tool after all and her usefulness was nearing its end.

Rei didn't know it, but Yui had seen her as she turned to walk away and she had seen the downcast look on her face before she disappeared around the corner.

* * *

Asuka was in a daze as she wandered through the maze of corridors that was NERV headquarters. She had spent almost two hours sitting in front of Unit 02, desperate for a sign that her mother was really there. She had begged and pleaded for a sign, for some form of acknowledgement that her mother was there and could hear her. She never got that sign, but somehow she knew that she was in there. She had to be. Now that the idea was in her head that it was a possibility, she couldn't accept anything else as the truth.

Like the bursting of a dam, the words and the emotions had flowed out of her in a torrent. She began to speak about her life. She said all of the things she had wanted to say to her mother, telling her how much she loved her and how badly she missed her. She talked about what she had done in the years since the day she found her hanging from the ceiling, the good and the bad. She laid herself bare and as her emotions continued to flow unabated, she found that she couldn't stop them. She simply couldn't contain them and hold them back anymore. She told her mother her true feelings. She was lonely and she was scared.

And through all of it, Asuka Langley Soryu had cried. More accurately, she had wailed, shedding all of the tears she had refused to let go of since her mother died. The last day and a half had served to break her down completely and the voice in her head kept telling her that it was alright to cry. But she couldn't allow herself to completely drop the armour that she had spent so long building up. She cursed the voice to no end, battering it back into submission, her head throbbing painfully as she fought with herself. She had vowed to never cry again after her mother died and that vow had just been shot all to hell. Instead of being a release, the tears only served to cause her more pain. She felt humiliated and weak and she despised that feeling.

Violent urges welled up inside of her, her temper seething and boiling over. She wanted to hit someone, to make them feel pain like she was feeling. She wanted to pound Shinji for showing her up, she wanted to pound Misato for stealing Kaji away. She should have pounded Dr. Akagi when she had the chance, she was sick of her superior attitude and her acidic rebukes when her sync ratio was down.

She stopped and leaned against the wall, her hands pressed tightly to her head. A groan escaped through her clenched teeth as she fought the blinding wave of pain that lanced through her head. As it slowly began to subside she caught a glimpse of something out of the corner of her eye and turned to see someone who she despised above all others.

Ayanami.

The blue haired bitch was exiting a stairwell that provided access to the medical wing. She had probably been sitting like a statue beside her Ikari-kun's bed. She would be so happy that her little friend, her only friend, was back. She began to move towards her, the voice in her head screaming at her, trying to stop her from what she was going to do. But she was beyond arguing with it now, the searing pain in her head was pushing her beyond all sense of reason or rationality. She ignored the voice as it screamed and begged for her to stop, to just turn and walk away.

She had just found her outlet.

* * *

 _ **Commander Ikari's Office**_

Self reflection was a rare practice for Gendo Ikari. He preferred not to look back on his life too often because it tended to promote the formation of a conscience and that was something he had grown to have little use or need for. It tended to get in the way and distract one from their purpose. Self reflection, coupled with an in depth discussion with a rather large bottle of sake, was something even more rare for him. It was something that he hadn't done in many years, as his aching head could attest to.

It was through that self reflection that he had seen just how absurdly far he had gone and how far he had been willing to go in order to be reunited with Yui. It didn't matter that the reunification may have only resulted in nothing more than the briefest contact between their souls before all became one and not the more eternal result he wished for. He needed it, and just like a junkie that need had consumed and driven him to do things that should never have even considered.

The idea that she wouldn't forgive him for the things he had done had certainly occurred to him just as all other possibilities had. He hadn't attained the position or the power he had today without thinking through every possible angle to everything he did and that applied to Yui as well. However, he had never thought that she would return alive and in the flesh, it had been too much to hope for and that made the whole idea of forgiveness for his actions a very real one and he _hadn't_ considered that.

But now he had to face the hard cold reality of that possibility. He had known about Fuyutsuki's visit and had heard his conversation with Yui. He had known about the loop the old professor had installed into the monitoring program. The nagging little voice of fear in the back of his mind had been right. She wasn't going to forgive him. He had pushed that painful bit of knowledge aside and gone about his day like nothing was wrong. After talking to Dr. Akagi and Chairman Kiel, he had set about devising new plans for the immediate future. When he returned home late in the evening he began his meeting with the sake bottle.

Alcohol had a way of making you reflect on things even if you were drinking in an effort to forget about them. Gendo wasn't drinking to forget, it had just seemed like the logical thing to do once he began to truly realize the full weight of the things he had done. The problem was, he wasn't entirely sure that he still wouldn't go through with the Human Instrumentality Project. It had always been his aim to do so, having hitched his wagon to SEELE long ago.

He still had Adam attached to his right hand. It was probably the worst decision he could make but he had decided, at least for now, to leave the Angel where it was. All options were needed no matter what he ultimately decided to do. Now that Yui was back could he still carry out such a plan just to save himself from the misery he was now feeling because he knew she wouldn't forgive him? That was the problem, he just might do it. He just might run away from the pain by ending human existence itself. What a lowly coward he had become, the same sort of human wreck he had been purposely turning his own son into.  
When he first came to know Yui Ikari he had desired to get close to her because of her existing connection to SEELE, the funding they put forth for her research, and the power they wielded. It didn't take long however for him to see her for the wonderful woman she was, a woman who loved him despite his unruly behaviour and personal insecurities. She was a kind and warm person who seemed to have a wisdom beyond her years. He had never thought of himself as worthy of being loved by anyone, a trait he had sadly passed on to his son, but Yui had indeed loved him.

Gendo knew that at his core he was a weak man and like all weak men with a measure of power, he was a bully. He was a ruthlessly efficient bully but still a bully none the less. When Yui had been absorbed into Unit 01 his world had disappeared with her and it changed him into something worse than he had ever been. He had become virtually inhuman, not caring who he hurt or how badly he hurt them. He used people until there was nothing left to use and then he threw them away without a thought. He realized too late now that he had been doing the same thing to both Yui's imprisoned soul and the son that was so precious to her.

Then there was Rei. It was bad enough that he had created a life in the laboratory after abandoning his own flesh and blood, but the things he had done to her. The isolated engineering of her personality to ensure her loyalty. The long hours she was made to endure in the process to download her experiences into the dummy plug system. The scorn that she experienced from others because of the way she looked and the way she had been made to act. Of them all, she had suffered the most because that was why she had been created. She was not to know joy or love or happiness or freedom because it had no part in her role within his scenario. She was nothing more than a tool he had manufactured and honed to his own specifications.

And he had felt absolutely no remorse what so ever for doing it.

SEELE's Human Instrumentality Project had given him the perfect opportunity to reunite with Yui. Except for the end result their goals and his were the same, so all he had to do was follow along and make sure the sanctimonious old fools didn't get wind of his plans and thus far they hadn't. They didn't trust him and they most certainly suspected he that he was up to something, but that was irrelevant so long as they thought they were still getting what they wanted out of him. He would gladly continue to use them and in the end he would make sure that Kiel and the others got what they so richly deserved. Even if he ultimately gave in to his own weaknesses and continued with the scenario, he was determined to make sure the old men didn't get things their way. And it was time to plan for that contingency as well as a couple of others.

Picking up his phone, he punched in the extension number he desired. It was answered on the second ring. "Agent Kaji," he spoke coldly. "Drop whatever you are doing and come to my office immediately. I have a job for you."

Without waiting for a response, he hung up the phone. Unlocking the central drawer of his desk, he pulled out a large calibre automatic pistol and laid it on the desk. He was going to make the spy an offer that he couldn't possibly refuse.

One way or another.

* * *

 **AN:** In the manga, we see Yui as being a full on believer int he concept of Instrumentality, seeing it as a way to make a better world for Shinji. Not exactly sure how that logic works considering what was going to happen, but there it is. In the anime we get a less clear picture of her thoughts and commitment and are left to formulate our own thoughts on it.

I am trying to use a blend of the two here. From both media we also get the impression that Yui is also a bit naive. She strikes me as a truly good and kind woman and not the type would go for the 'bad boy', but she ends up with Gendo. And despite her obvious intelligence her belief in Instrumentality being beneficial for Shinji and his future screams naivete. She isn't a mad scientist type but her adherence to what she's working to accomplish has a similar flavour. Without the evil component of the mad scientist, you get a naive individual who thinks they are doing the greatest thing for mankind that they can possibly do.

Poor Shinji. He wanted her back so badly and now he has her and he wants so badly not to hold her responsible for her actions. It's so much easier to blame Gendo...he is and always was a bastard so he is the easy fall guy and he deserves to be. Even before he lost Yui he used people and was not well regarded. He's always been a bastard.

We always suspect that deep inside Shinji must have a very deep well of anger hidden away and we often speculate how much of the berserker state of Unit 01 is influenced by it. Will Shinji show any actual anger in regards to his mother at some point in this story? It might be addressed at some point and in some way before the end. Just don't expect an outright scream fest. That's as close to any kind of a spoiler as I will ever give.

With that said, please leave a review if you would be so kind.

And while you're here, check out my other stories.


	5. Chapter 5

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

 **Transposed**

 _ **Chapter 5**_

 _ **Shinji's Hospital Room**_

To say that Shinji was stunned and overwhelmed would have been the most severe understatement of the century. Trembling, he sat with his back to the head of his bed, staring blankly across the room while his mother sat beside him with her arm around him. Sub Commander Fuyutsuki had just left after telling them the truth, the whole truth, behind everything at NERV. The Evangelions. The Angels, including the one in Terminal Dogma and the one attached to his father's hand. NERV. SEELE. Third Impact and Instrumentality.

Rei.

He didn't think it was possible for him to be able to dislike his father to a greater degree than he already did, but he discovered that he was quite mistaken about that. Any desire that he had ever had to hear his father praise him and accept him was now long departed from his mind. It didn't matter what his motivations had been, there was nothing he could ever say or do now that would make him have that desire again. How could he have respect for, or desire anything positive from a man who was willing to destroy the entire human race for his own selfish purposes?

He had manipulated every person he had contact with towards that end, including his own flesh and blood. He couldn't begin to understand how his father could possibly do all of the horrible things he had done, how he could have wanted to do what he was planning. Did he really view human life as being worth so little? The lives he had manipulated and ruined, all of the people that he had hurt, he could barely comprehend it. His abandonment had been part of the plan all along. One of his worst recurring nightmares was the memory of him crying for his father not to leave him, but having him calmly turn and walk away without looking back. To now know that it had all been part of his carefully crafted plans made it hurt all that much more.

The puzzling thing for him however was that he hadn't completely gone to pieces when he heard it. Either he had become immune to how low his father could be, or his mother's presence had helped him to keep himself together. Maybe, it was just the shock value of it all, but so far he had managed to keep himself together and hadn't crumbled into a pathetic, sobbing heap. He was however, not very far from it.

Equally as incomprehensible to him as his father's actions, was that an organization like SEELE could even exist, let alone have the power and influence they had held over so many people for so long. Perhaps he was just naive to the realities of what went on in the world, but he couldn't help but wonder how such a group of men could come to hold so much power and how they had been able to keep it without the rest of the world knowing about it and putting a stop to it.

They had been able to cover up the true nature of Second Impact and they had been able to make plans for a Third Impact without making anyone suspicious enough to look into their activities. Maybe it was because they were able to take advantage of the world while most people had placed all of their focus on just trying to survive in the aftermath of Second Impact. He wasn't even sure that he really wanted to know the answer.

The thing that shocked him the most on a personal level however, besides even the truth about his father, was the revelation of who and what Rei really was. That was the biggest thing that was giving him the thousand yard stare right now. It seemed to be hitting him harder than everything else, probably because it was so personal. At least he now understood why Rei acted the way she did. She simply had no other choice and didn't know any other way. Since she had been denied everything that made up a normal life she had been kept from the experiences that everyone else took for granted. She had so little experience with life and the world in general, she probably didn't even realize just how badly she had been treated.

It horrified him to think that his father would artificially create a life like that just so he could manipulate it to suit his purposes. He created her to die for his purpose and she was willing to do so because that was all that she knew, all that she saw as her purpose in life. She was disposable and easily replaceable by another copy. She was the basis of the dummy plug system. It all made his stomach clench and he had to try his hardest not to throw up.

From his own personal perspective, he didn't know what to think about Rei now. Before the events of the last few hours he knew that he liked the quiet, blue haired girl. He _really_ liked her, but he had never been able to find the courage or the words to say so. He had never been put off by her pale appearance, her blue hair or her red eyes. As a matter of fact he liked the way she looked. She was exotic and he thought her eyes were beautiful. He just wished he had the courage to look into to them when he was around her.

Now he didn't know how he should view her and he was ashamed that he even had to think about it. She wasn't the enemy, she was his friend and he wished she was more than that. But how could he have such feelings for her when he knew she had been created from the manipulated DNA of an Angel? The revelation that she was indeed an angel, or at least a hybrid of one, quite frankly scared the hell out of him. She did have a semi functional S2 organ occupying the place where a human female's ovaries would be. It allowed her to heal faster, but it wasn't powerful enough to produce a blue pattern that would set off the Angel alarms.

To ensure that her S2 didn't fully develop she was required to take medication each day to keep it in check. It slowed the development but it couldn't stop it and the organ continued to slowly grow towards maturity. Despite those facts, she looked human. The Sub Commander had said it was because she had been cloned from the Second Angel herself, Lilith, the progenitor of humankind. Some human DNA was added to stabilize her form. Possibly even DNA from his mother, but it would be impossible to tell that now since her Angel DNA had long since assimilated any genetic material foreign to itself after taking on its physical traits.

His mind was still having trouble coming to terms with all of that. It was way too much for him to process so quickly, especially considering his feelings for the girl. She was a clone, a manufactured being, and an Angel as well. Regardless of that he still had strong feelings for her in his heart. He was ashamed of himself that he couldn't seem to put all of those other considerations out of his mind because of the untainted honesty of those strong feelings.

He had always felt drawn to Rei. Was it because she seemed to be as empty as he felt? Did it have anything to do with the possibility that she had been created at least in part, with influence from his mother's DNA? Did any of it even matter or mean anything at all? He didn't know, he couldn't explain it, he just knew that he had always been drawn to her, still was even now after hearing everything he had just been told about her. He still wanted to be her friend but he also now felt fear of her begin to creep into his heart. It all left him feeling sick and confused and more than just a little bit heartbroken.

He could say that he also felt the same way about losing Misato to Unit 01. He had a special kind of love for his guardian, she was both his best friend and sort of a goofy big sister to him. She was the only person who had shown any concern and affection for him and who had told him that she was proud of him. She may not have always know what she was doing in regards to being his guardian, but she tried and that was more than anyone else had ever done. It was her tearful and anguished cries that had made him decide to leave the Eva's core. Actually, now that he thought about it, he was sure he had heard Rei's own quiet voice as well, beckoning for the Evangelion to let him go and return him to her.

He didn't like to hear Misato cry, but her tears had told him that someone would actually miss him if he didn't come back. In her own way she needed him and he needed her. They had become inseparable in their own strange way, connecting in a way he wasn't sure he could explain. He supposed that in some mixed up and awkward way he actually loved her and he couldn't imagine his life anymore without her in it.

When his mother told him that Misato had pushed her out of the core behind him and had taken her place, he found himself feeling a new level of respect and appreciation for the purple haired beauty along with his fear for her well being. You didn't make that kind of a sacrifice for someone if you didn't care about them and as sad as losing her was, it felt good to know that she cared so much.

He also found himself feeling something else he had never felt before, an actual desire to get into Unit 01 and sync with it. His mom had told him that Misato would have a fight on her hands trying to get the core consciousness to accept her and he was worried about her. He wanted to sync and try to find out if she was okay. He needed to know. He didn't know if she would hear him or not, his mother said she would, but he also wanted to thank her, to tell her how much it meant to him to have his mother back in his life again.

"Shinji?" his mother worriedly called, giving him a gentle squeeze and breaking into his thoughts. "Are you alright love?"

"How could father do so many terrible things to so many people?" he asked, his voice quiet yet ragged.

"He became obsessed," she answered with a sad tone in her voice. "He couldn't accept that I was gone and he was willing to sacrifice the world to try to be with me again. I'm so sorry Shinji, I never thought that he would abandon you and treat you the way he did."

"It's not your fault Mom," he tried to assure her.

"But it is," she countered. "I let the Eva take me, it's what I had planned all along. I was thinking too much like a scientist who happened to be a mother and not enough like a mother who was a scientist. I thought your father would look after you and help you to become strong."

"But you couldn't have known that he would abandon me." His tone was pleading. He didn't want her to blame herself for something that he felt his father was solely responsible for.

"But I abandoned you too Shinji," she sobbed, tears beginning to fall down her cheeks. "I'm the one who ultimately put you inside the monster and caused you so much pain. I thought that I could ensure your safety when the Angels came because you would be the only pilot I would accept. But all I did was hurt you. I love you so much, more than anything else that exists, but I am the one that did this to you. I'm sorry Shinji, I'm so sorry."

He hugged her tightly. "Don't say that Mom. You didn't abandon me. You did this to protect me. You didn't think you had a another choice."

It was heartbreaking that in his desperation to be with her he couldn't see how thoughtless and cruel her actions had been to him despite how heartfelt, honest, and obviously misguided they had been at the time. He couldn't see what a horrible thing she had done to him.

"I should have found one Shinji, I should have found another way to make the Evangelion work so that I could have stayed with you," she cried. "If I had, you wouldn't be so scared and lonely. You wouldn't think so little of yourself. You would have been hurt so much."

He didn't know what to say or do to make her feel better or to make her believe that none of what had happened to him in his life was her fault. Obviously he would have preferred if she hadn't given herself up to the Eva, but she had done so to try and ensure his future and he wasn't going to hold that against her. She did what she did because she loved him and knowing that, despite all of the pain and loneliness he had endured, it gave him a good feeling. It made him think that maybe there was hope for him to find some happiness in his life after all now that he had her back. He didn't care what she had done.

For her part, Yui was trying very hard not to lose what little composure she had left as she clung to her son. Triggered by her feelings of guilt, the emotional weight of the last ten years was settling in on her and threatening to smother her. For Shinji's sake she didn't want to break down any more than she already had. She hadn't told him much yet about what it had been like inside the core, especially early on, and if she could help it she would hold off on that at least until they found out if Misato was still 'alive' inside Unit 01's core.

Besides, there was more to her emergence from the Eva than anyone knew. It was the thing that she had felt she was forgetting since she returned and she couldn't let it be known. Not yet, and she certainly didn't want to tell Shinji yet, he would only worry and be distracted from what was to come. He was needed both to fight the Angels and to establish a synchronization with his guardian who she knew he was very worried about. That synchronization would help keep Misato from losing herself to the awesome consciousness that was contained within Shogoki's core.

The only survivor of the Katsuragi Expedition had her strengths, but she was also very fragile as well. Yui well remembered the sight of that broken girl in the isolation ward of the NERV medical centre and she had wanted to take her in and make her a part of the family, but Gendo had been against it. She had always felt guilty about not doing something for her and now that she was in her current predicament she felt even worse. She hoped that Misato could hang on.

Initially, after she had allowed the Eva to take her, her conviction as to what she was doing and why had been enough to sustain her, but it became harder and harder to hold onto that as time passed. She loved her son with everything she was and it was hard to leave him and to miss so much of his life. As she became more aware of events around her she had begun to wonder if she had done the right thing after all. By the time Shinji first synced with the Eva, she knew without a doubt that she had made the wrong choice. The worst choice possible in all regards.

She had counted on Gendo to look after Shinji. She had counted on him to raise their son to become a strong, confident, and capable young man. She had hoped that Gendo would tell Shinji what was happening and that he would bring him to train to use Unit 01. She waited for ten long years to see her son again, worrying all the while about his well being. When he finally came to Tokyo 3 she was horrified to see how Gendo treated him and it only got worse when she touched his mind when they synced. Gendo had done the unthinkable, he had abandoned her precious little boy just as she had. He had set him on the road to psychological ruin so that he would lose the desire to live and could be used to trigger the end of mankind.

They heard the door open and turned to see the focus of their anguish standing in the doorway. Gendo was trying hard to maintain his cool and commanding exterior, but it was obvious that he was off his game. It didn't help that he was receiving a very cold stare from Yui and an extremely hostile one from his son.

"Shinji," she said quietly. "Could you give us some time to talk?"

His righthand began to open and close reflexively. "I don't want to leave you here with him," he virtually growled, never taking his eyes off of his father.

She gently stilled his hand with hers and gave him a soft smile. "It will be okay Shinji. I'll be fine."

Reluctantly, he left her side and headed for the door. Not once did is eyes leave those of his father's and the glare he gave him was as bad as anything Gendo himself had ever displayed. Without saying a word, he left the room.

For a long while they just looked at each other. The words Gendo had been prepared to say had withered away under the cold stare she was giving him. As for Yui, she wanted to say everything and nothing at the same time. How did you address someone you once loved who had done such terrible things and ruined so many lives, including the life of his own son?

"Needless to say, it is good to see you again Yui," Gendo finally spoke. "I have missed you terribly."

"Has it been worth it?" she asked him, making him stiffen at the force behind her words. "The lies, the deceit, the ruined lives. Rei. Shinji. Has it all been worth it Gendo?"

"All I have ever wanted for the last ten years was to see you again, even if it was a fleeting touch of our souls before all became one," he began. "And as horrible as it may sound, now that you are here, alive, I have to say that it was."

She wasn't exactly sure what she had been expecting him to say, but that wasn't it. It nearly rendered her speechless.

"I also realize that what I have done cannot be forgiven, no matter what I do from this point on," he continued with a slight frown. "It took a long night and a hangover to make me realize exactly what I have become."

"What you became was yourself," she said bitterly. "What you've always been. In the beginning you sought me out because of my connection to SEELE through my grandfather, and because of my research. You used Fuyutsuki to get to me, and you used me to get to SEELE and GEHIRN. I was your inroad to all of this."

"I loved you then Yui, and I love you now," he told her. "I had always believed that I could never be loved by anyone, but you showed me otherwise."

"And that's one of the reasons why I'm so appalled by the things you have done Gendo," she said quietly. "Because I did love you. I defended you. I told everyone that they were wrong about you, that they just didn't understand you. When they said you were only interested in me because of my connections and my work I told them they were wrong. I should have listened. I was so naive back then."

He decided to be totally honest with her, there was no point in lying about it. "They were right about me," he admitted. "I saw an avenue to power and prestige and I followed it. But along the way I discovered what a kind and compassionate woman you were and I fell in love with you. You were the lone bright spot in a world I saw as being dark and filled with nothing but pain, suffering, and loneliness."

"Even so you still thought Instrumentality was the cure for the world," she said. "And I was foolish and naive enough to fall into that trap as well. I let the thrill of scientific discovery and the list of accomplishments we were achieving blind me to the truth. I even let myself give credence to the Committee's party line that what we were doing was to end mankind's pain and suffering," the look on her face became even angrier. "I was so full of myself and the fantastical vision that I had created that I didn't see it for the pack of lies that it was. Nothing but a bunch of frightened old men, terrified of their own mortality and looking for a road to eternal life and godhood and I fell for it thinking I would be somehow giving Shinji a better future."

She turned her gaze directly back onto Gendo. "When I let the Evangelion take me you decided to tailor the project to suit your own purpose. You used my desire to protect Shinji to try and enact your own Instrumentality scenario, just so that you could see me one last time before all became one. Something that wasn't even guaranteed."

"I fell apart," he admitted. "The only support I ever had, the one thing dearest to me was gone and I saw no reason to do anything else."

"You had a reason Gendo," she seethed. "And his name is Shinji. Not Third Child, not Pilot Ikari. Shinji. You had a son who needed you and you walked away from him as he cried for you not to leave him. He had to practically raise himself and spent years wondering why his father didn't love him."

"I couldn't …"

"I don't want to hear it!" she yelled, her temper finally getting the better of her. "He needed you and you left him! Even so, he still hoped you would acknowledge him and continued to do so right up until you used that damned dummy plug. And what about Rei? You wouldn't look after your own son but you created her, raised her and made a tool out of her. You ruined Shinji's life and you never even let her have one."

"You left him as well Yui," he countered sternly. "You knew what would happen that day, yet you insisted that he be there to watch. You love your son so much, but you let him watch you be taken away. You let him watch you die."

"Yes, I did," she admitted tearfully. "And it was the worst mistake I have ever made in my life. I spent ten years waiting for him and I had more than enough time to begin realizing just how wrong I had been about it all. I will spend the rest of my life regretting it in shame and I will do everything I possibly can to try and make up for it. I may have left him...yes, I abandoned him, and I was so wrong to do it, but at least I didn't throw him away like he was garbage. I didn't try to make him loathe himself so much that he would wish to die and take the world with him." She levelled a steely gaze at him. "Are you going to throw Rei away as well now that the purpose you created her for is no longer there?"

Gendo froze momentarily. With all of the commotion of Yui's return and his near momentary psychological paralysis over it he had overlooked something, which was definitely not normal for him. He hadn't seen Rei since before the last retrieval attempt. Her sole purpose for living, the one that he had drilled into her as being the only thing that should ever matter to her, was now gone. With that purpose gone she would not know what to do, she would have no direction and would be questioning her continued existence. The fact that she had been displaying a little more in the way of emotions lately would only make her situation that much worse.

Yui noted the look on his face with disgust. She recalled the distressed look on Rei's face when she saw her earlier in the hallway. "You haven't even spoken to her since we came out of the core have you?"

"I've been trying to keep Kiel and the Committee at bay," he explained by way of defence. It sounded weak even to him. "They are asking questions that I do not yet have answers for."

She would have responded with a disgusted comeback, but a sudden commotion out in the hall interrupted their conversation.

* * *

 _ **Inside Unit 01**_

The already dim, reddish hue of her surroundings brightened marginally as Misato felt the presence approaching her. The air seemed to become cooler and she felt goose bumps rise up on her naked flesh. She may not actually be in her body, but apparently the sensations were all the same to her soul. A breeze swirled around her, just enough to toss her hair a little and send a chill rocketing down her spine. A chill that had nothing to do with the temperature.

"So, it looks like I have someone new to share this space with," a cold, disembodied, female voice echoed around her. It was impossible to truly tell which direction it was coming from.

"Where are you?" Misato asked, trying to keep her fear restrained. "Show yourself!"

"I am all around you Misato Katsuragi," she voice answered. "And you are in no position to be making any demands of me. You are in my domain and nothing happens here unless I allow it to."

"So you brought me into the Eva?"

"Yes," the voice confirmed.

"Why?"

"Does it matter?" The voice sounded slightly amused. "You wanted me to let him go and I did. I even allowed you to send his mother back with him."

"That doesn't explain why I'm here," Misato spat, her irritation growing. "And why was she here? Am I supposed to replace her then?"

"Do you think that you can?" the voice taunted. "Do you think that you can be the buffer between me and my pilot? Can you meld your will with mine and act as the soul of this beast and his instrument of destruction?"

"I'll do whatever I have to," Misato answered defiantly despite the fear that was gnawing at her insides.

The voice laughed mirthlessly. "You certainly will at that, won't you?"

Misato saw something emerging from the shadows in front of her. It was a woman, naked just as she was, the shadows seeming to flow around her like a living fog. Her heart skipped and her breath caught in her throat when she saw the woman's face.

It was her own.

* * *

 _ **NERV Medical**_

After reluctantly leaving the room, Shinji had moved a short way down the hall and sat on a bench by the windows. The artificial late morning light illuminated the beauty of the Geo-front, but his eyes saw none of its splendour. He was barely holding himself together. So much had happened in such a short time and he had learned of so many unbelievable things. He felt like his brain was going to explode like an N2 mine.

And he was so very angry.

The moment he saw his father standing in the doorway he saw red. Instead of feeling intimidated and uneasy like he normally did in his presence, he felt like going berserk on him, tearing the flesh from his bones with his bare hands for all that he had done. The feel of his mother's touch gently stilling his clenching fist was the only thing that had stopped him.

Still, he didn't like the thought of her being alone in the same room with him. His plans may have revolved around seeing his mother again, but he had absolutely no trust in that man. He didn't even want to refer to him as his father anymore. As far as he was concerned, he had no father. It wasn't very hard for him to see it that way since he had never been much of a father figure to him in the first place.

It was inconceivable to him that his father could ever have thought that mother would accept him after all that he had done. He couldn't help but think how the lives of all of the people around him would be different if it hadn't been for his father's influence. Then again, maybe things would still be the same because even if his father hadn't been involved, there was still SEELE.

"Sub Commander Fuyutsuki said there would be three more Angels," he said quietly to himself. "I hope we can handle them." He thought it would be just his luck that now that he had his mother back, one of the Angels would finally succeed in killing him.

"Leave me alone!" a familiar voice shouted from a short distance down the hall. While the voice was well known to him, its current tone wasn't. I sounded ragged and anguished and very much afraid.

He looked to his right in the direction of the nurse's station and saw Asuka lurch away from an orderly and sort of half stumble, half shuffle her way up the hall in his general direction. He was shocked at the way she looked.

Firstly, she was crying and her eyes were red and puffy. Asuka _did not_ cry. _Ever_. Her hair was a tangled, disorderly mess and her cherished neural clips sat askew on her head. Her school uniform was rumpled with one shoulder strap hanging down her arm and stained with something dark as were her hands. It wasn't until she got closer that he could see that the stains were blood.

"Asuka!" he exclaimed, rushing over to her. "What happened? Are you alright?"

Her eyes were unfocused and she seemed like she didn't really know what was going on or where she was. "Asuka, what happened?" She was really starting to freak him out.

She stopped and her eyes drifted up to his face and she stared at him. For a moment it seemed like she didn't even recognize him. "I…," she began. She seemed to be having trouble connecting her thoughts and stringing the words together. She frowned. "I hurt her." She said it so quietly that if he hadn't been standing right in front of her he wouldn't have heard it.

"Who? Asuka, please, tell me what happened?" he pleaded. He felt the urge to grasp her by the shoulders as if he could put her at ease and get her to tell him but past experience reminded him that touching Asuka without her permission was strictly verboten and would carry very painful consequences.

She raised her shaking bloodstained hands and stared blankly at them. "She didn't fight back," she said, her voice wavering. A fresh stream of tears cascaded down her flushed, blood flecked cheeks. "She didn't defend herself or try to run. She didn't cry or scream….she didn't say anything at all. Nothing. S-she just let me keep hitting her and hitting her."

"Asuka…." he started.

"Why!" she suddenly yelled, startling him. A bit of the anger he was used to came back to the surface, mixing with the pain and confusion that was so evident on her face. "Why would she do that! Did she want to die?! Di-did she want me to beat her to death?!"

He was stunned at what he was hearing, and he suddenly got a very pronounced sick and sinking feeling in the pit of his stomach. "Asuka, who's blood is all over you? What happened?" he pleaded.

Her demeanour went back to what it was before the angry outburst. A fresh flood of tears streamed down her face and she began to tremble even more. Her eyes went wide, as if she had just realized something.

"Mein Gott," she gasped. "T-that's what she wanted." The look on her face quickly became one of horror and her voice dropped to a ragged whisper. "Wondergirl…w-wanted me to k-kill her."

Shinji was too shocked to utter a sound. His already overworked mind was having great difficulty processing her behaviour let alone what she had just said and he certainly hoped that he had misheard her. Her eyes became unfocused again and when she spoke he was only just able to make out what she was saying.

"I want my Momma back too," she sniffled. "I love my Momma and I miss her so much. How come you got your Momma back but I can't have mine?"

He was stunned beyond belief and was completely at a loss as to what to do or say at this point.

She suddenly became very wobbly on her feet. She sniffled and scrunched up her brow, her right hand going up to rub the side of her head and she whimpered slightly.

"My head hurts," she cried, sounding very much like a scared little girl. Her eyes rolled back and she lost consciousness, toppling right into Shinji and sending them both to the floor. He heard a loud crack and felt a sharp pain in the back of his head before everything went black.

* * *

AN: The question of Rei's genetics is one of NGE's biggest screw ups. Not once in the 26 episode run of the series was it ever mentioned. It didn't come up until someone created what is known as the Red Cross Book. Essentially it was pamphlet containing a glossary of terms for things people may have needed a refresher on the meaning of when the movie End of Evangelion came out. (It wasn't until Rebuild 3 that they finally came out and actually said she was a clone of Yui, but rebuild isn't exactly canon to the rest of the series)

Twelve whole words were devoted to the explanation of Rei's genetics in the Red Cross Book (shitty pamphlet!). I'm sorry, but this is not how you make something canon and this was just about the most ridiculous way to do it. However, rather than blatantly argue against it, I decided to split the difference and I came up with a way around it that I think is plausible.

* * *

Please leave a review if you would be so kind.

And while you're here, check out my other stories.


	6. Chapter 6

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

 **Transposed**

 _ **Chapter 6**_

 _ **Kaji's Apartment**_

Kaji leaned back in his chair, regarding the information on his desk and on his computer screen like it would leap out and devour him at any moment. He wasn't entirely sure that it wouldn't. He fumbled in his shirt pocket for the crumpled pack of cigarettes and his lighter, shakily torching the end of one and taking a deep drag, exhaling it with a weary sigh.

Before him were the complete plans for the Human Instrumentality Project, both from SEELE's perspective and Gendo Ikari's. For years he had been seeking this truth and now that he finally had it he didn't know whether to laugh, cry, or throw up in horror and disgust then go curl up in a dark corner. All of the above followed by a quick descent into insanity did not seem out of the question at the moment.

"So this is the reason for everything," he muttered in disgust. "Second Impact was deliberate, Adam, which I brought to Ikari, was a major catalyst for his plans, and the giant on the cross in Terminal Dogma was actually the Second Angel, Lilith. The Evangelions are made from the first two Angels. Caged Angels to fight other Angels, piloted by children protected by the souls of their mothers…."

He had to swallow hard to keep from emptying his stomach across the desk.

"I never imagined that it was anything like this." He took another long drag, filling his lungs with smoke. Reaching into a desk drawer he pulled out a half dead bottle of rum, unscrewed the top and took a long pull.

"Better not get drunk," he mused as he recapped it and set it aside. Though it sounded like a hell of an idea. Maybe later, if he survived. "I've got way too much to do."

It had never entered his mind that giving him the truth was what Gendo had in mind when he summoned him to his dark lair. But sure enough, there the man sat with a stack of files, a couple of computer disks, and a pistol laying on his desk. At first he thought he was a dead man until Gendo asked him one, simple question.

"Do you want the truth?"

He did, and always had, and he would have sold his soul to get it. In some ways he supposed that he already had. He knew there would be a price to pay for Gendo giving him this knowledge, and it came in two parts, both of which surprised him. The first was that Gendo wanted him to be his safeguard should he try to continue with the plans he now had before him. The second part was to get the information about SEELE's plan to someone in the UN that he was positive was not in the Committee's back pocket.

After Gendo told him what the plans entailed and why they had been created in the first place, he was speechless. He also realized that he would have been stone cold dead long before he ever could have pieced together enough of this on his own to take it to the UN and put a stop to it. Ikari had essentially just given him the keys to bringing down the kingdom.

"For SEELE it was all about forced evolution and becoming as God," he thought aloud. "For Ikari it was that at first before it became all for the love of a woman that he could not live without." He shook his head in disbelief. "The planet tilted off its axis and forever changed, three and a half billion people dead, countless others manipulated like chess pieces so that their scenarios would continue to advance unabated."

He had asked Ikari why he was to only expose SEELE as the masterminds and overseers of the plan and not disclose that he had his own separate scenario working within theirs. The response he had received was most definitely not one that he expected from the man.

 _'I do not wish to cause any further harm to the people I have used. They would all have to live with the spectre of my actions for the rest of their lives whether they were aware of their roles in my plans or not. They would always be suspected of being willing participants rather than having been manipulated as pawns to facilitate what I have done. It was always SEELE's scheme before I ever became involved, let them suffer for it.'_

They both knew that it was inevitable that no one from the command staff down through the pilots would escape suspicion anyway, be it public, private, official, or unofficial. It was naïve and foolish to believe otherwise. But if Gendo went ahead with this and didn't change his mind and went ahead with Instrumentality anyway, it might take some small measure of the heat off of everyone else, at least as far as the law enforcement agencies that would be investigating were concerned. Public reaction once the story got out would be a different and very ugly response entirely. Supposedly that was why he wanted Kaji to be his fail safe and he would be with one exception that he hadn't told Ikari about.

He would not shield Ikari's involvement in this as he had requested. To him it seemed like Ikari was just giving himself another potential way out so he wouldn't have to admit to it all in the end. While the authorities chased SEELE, Gendo could continue to operate unopposed and the Old Men would be too busy trying to evade the law to interfere with him. He could then either carry on towards Instrumentality or disappear into the night when everything was done. He didn't see Ikari as the type of man who would stand and accept the consequences for all of the horrible things that he had done.

Shielding Ikari would do nothing for anyone else but Ikari, it wouldn't lift the weight of scrutiny off of anyone else in the slightest and he didn't believe for a moment that Gendo actually cared about anyone else enough to ever do this for the reasons he tried to sell to him. It was a hollow gesture that in the end would benefit no one. The fact of the matter was that there was only one irrefutable reason for him to be proposing something like this in the first place and that was the return of Yui Ikari.

Her emergence from Unit 01 had shaken him to his very core and even if she didn't forgive him, and Kaji highly suspected that she would not, the mere fact that she was back among the living looked on the outside to have changed the Commander's perspective on things and had caused him to seemingly have an attack of conscience of all things. During his meeting with him he definitely saw that Ikari did not seem to be thinking or acting quite in the way he was accustomed to. As controlled as Gendo was, he had seen the small signs that spoke volumes. The man was still in a state of shock and acting in a way that seemed to be far from his usual calculating and rigidly precise manner. He doubted it would last long though.

Personally, he wasn't convinced that her reappearance would be enough to placate him. Not now and he knew just enough about Gendo's history to know that he had no great love for humanity as a whole. He had planned and schemed for far too long and invested too much of himself into his precious scenario to merely be happy that his wife was alive and in the flesh again and not happily at his side. Hell, even if she was that might no longer matter to him. Quite simply, he didn't trust Gendo Ikari not to go ahead with it anyway. If he were a betting man, he would wager heavily that the Bastard King would indeed still go through with it once he got over his shock and reassessed his position and his options.

Then again, he knew the human conscience could be a powerful thing and there was always the slim chance that the reappearance of his wife had made Ikari rediscover his. The call of his after all had been the reason for his entire quest for the truth. He had betrayed those closest to him in those tough times right after Second Impact and their blood was on his hands. Seeking the truth was his way to try and atone for what he had done. No matter what Ikari was thinking or intending, he was not going to play his games now that he had the truth in his hands.

Considering the reasons why this truth was now available to him, he couldn't help but think about Misato and her current predicament. While she too was someone he loved, he had betrayed her as well by not being able to say the words to her that she so desperately needed to hear. The day that she left him he didn't even try to stop her. He never said a word to make her stay.

How could you claim to love someone, let alone tell them so, when the only thing you had ever done for them was help them willingly debase themselves and cover themselves in filth? Even now after coming into each others lives again, all he had offered her was sex when what she really needed was what she had always needed. Something he still couldn't give her, something that he doubted he was even capable of giving anyone at all. She needed someone to love her. Even Shinji had offered her far more in that department than he ever had, even if the boy didn't realize it.

He had watched Misato suffer while Shinji was locked away inside the beast. He saw just how much of her heart she had invested in that young man, like Shinji was the last chance she would ever have to be happy. He sincerely had hoped that Ritsuko could get him out of there, for Shinji and Misato's sake both. If Shinji was gone, he knew that would be the end of Misato. She would spiral so deeply into a pit of alcohol and despair that she would never survive and crawl back out again.

Now Shinji was back and she was trapped inside the beast instead. That woman had been through more than enough hell in her life already, why now this? What had she ever done in her life to deserve all of the pain and misfortune that seemed to befall her? For that matter, what had any of them done to deserve being under the thumb of people like Gendo Ikari, Lorenz Kiel, and the old farts of SEELE? Mankind's fault for not paying attention to the vipers in their midst he figured.

He stubbed out his cigarette in the half filled ashtray on the corner of his desk and pushed himself out of his chair. He walked to the bathroom and pulled a bottle of aspirin from the medicine chest, tossing a couple back and washing them down with some water he cupped in his hands. He splashed some cold water on his face and looked into the mirror, glad to see that he didn't look quite as tired or as old as he felt at the moment.

After drying off, he went back to his desk. He had copies to make of the information he had been given and he needed to go through his list of contacts to figure out who he could trust enough to give this information too. If he could stay alive and out of SEELE's reach long enough to do it.

* * *

 _ **Private Office of Lorenz Kiel**_

The head man of SEELE leaned back in his chair as the holographic meeting room in front of him faded into nothingness. The meeting had not gone smoothly. The other members of the Committee were becoming increasingly paranoid and irrational and viewed even the smallest problem as meaning disaster to their plans. They seemed to have lost any and all ability to see beyond the immediate problems and their perspective was becoming so narrow that they were endangering their long sought plans all by themselves.

He was sick of them all.

Though to be honest, the current kink in the plans was not an insignificant one. The First Child was lying unconscious in a hospital bed after being nearly beaten to death by the Second Child, who was currently in a hospital room of her own, sedated and under observation. And it was still unknown if Unit 01, the lynch pin to the entire plan, was even capable of operation.

Ikari had once again insisted that Unit 01 would still operate. He had an activation test scheduled for the next morning and he seemed otherwise unconcerned about the status of the other two pilots. Kiel figured he had adopted that attitude for no other reason than to send the more reactionary members of the Committee into an uproar, forcing him to reign them in and thus cut off Ikari's participation in the meeting at that point.

Even if Unit 01 activated and could still be used, they were still in a precarious position. The Angels kept getting tougher and with only one Evangelion to deploy, the odds didn't look good. While it was in his plans to eventually send Tabris into the fray in some manner, he didn't want to make that move so soon. Too many things could go wrong. For now, they had little choice. They would have to continue to trust that Ikari knew what he was doing and wasn't about to stab them in the back, though Kiel was sure that the man was indeed up to something and always had been.

It had been difficult to persuade the other members of the Committee to continue to stay the course and he had needed to resort to hammering them with his authoritative presence to bring them into line. It was something that was all too frequent a necessity these days and he was wondering if it wasn't time to make a couple of them disappear.

As delightful as that sounded, he knew that it probably wouldn't help matters any and he could put up with them until the project was completed. They had all joined willingly, putting their vast wealth, power, influence, and knowledge into the quest to free humankind from the bonds of its stunted evolution. Soon enough, they would see mankind be relieved of its pain and suffering and move on to the next stage.

Humankind would unite into one god-like being, no longer subjected to its emotionally and physically fragile nature, no longer even bound to the Earth itself. They would be free of every chain that bound them and have power beyond belief. All as one. And a very specific one at that.

 _If_ they could defeat the angels first, and the current situation was threatening to throw a monkey wrench into the works. More pressure would have to be applied to Ikari to ensure things continued to progress and if that progress was not forthcoming or satisfactory, then he would have to be replaced.

Even if he had to do the job himself. Regardless, he would have things his way.

* * *

 _ **NERV Medical ICU, Rei Ayanami's Room**_

Shinji had entered the room five minutes earlier, but hadn't moved much beyond the closed door since then. Besides the lump on the back of his head and the dull, muted ache emanating from it, he was feeling a number of different things. Bewildered and shocked was a good start. So many things had happened and so much startling information had been given to him in such a short space of time that he was overwhelmed by it all. The most prominent at the moment was the revelation of what the girl before him really was.

He knew it shouldn't matter. She was the same person he knew before he found out. He still thought she was pretty and he still had very strong feelings towards her. Even so he found himself afraid to approach her even as she lay there unconscious. The fact that she wasn't awake didn't make it any easier to approach her, nor did the fact that she was a mess.

Asuka was indeed very good with her fists and feet, especially when fuelled by her intense fury, as Rei's many injuries could attest to. The pale girl's face was swollen and bruised, with cuts around her eyes, her nose was broken, and her lips were split. She had several broken ribs and numerous other bruises all over her body. It hurt to see her like this.

He wanted to be angry at Asuka for doing this to Rei, and to a certain degree he was, but it had been pretty evident that something had gone terribly wrong inside the mercurial red-head's mind. He knew that she was certainly capable of hitting others, he knew it all too well considering how many times he had been on the receiving end of her displeasure. Despite that, he had never known her to go beyond a single slap or punch to make her point and she had to be pretty angry to go that far.

He finally willed his legs to move and slowly approached Rei's bedside. The closer he got, the worse her injuries looked to him and he nearly stopped again. He kept going but had to swallow a rather large lump that had formed in his throat. How could someone take a beating like that and never say a word? Not even to cry out in pain, or to beg for it to stop? Why hadn't she tried to defend herself? Why hadn't she run away?

"Ayanami…" he little more than whispered as he stopped at her bedside. He really didn't know what to say, so he went with what he did best. He apologized for something that wasn't his fault.

"I'm sorry Ayanami," he began. "I never thought Asuka would ever do something like this. S-something happened to her. I…I think she found out that her mom is in Unit 02 and it was too much for her to take."

He closed his eyes and had to swallow that annoying lump again. His right hand began to reflexively clench and open, clench and open. He didn't even realize he was doing it.

"Why didn't you fight back or defend yourself?" he asked, trying very hard not to start crying. "Did you really want her to kill you? Do you hate what you are that much?"

He suddenly froze in horror. His eyes going wide. That was not what he intended to say but it somehow managed to escape his mouth before his brain could filter it. ' _Do you hate yourself that much?',_ or _'Do you hate your life that much?'_ , was more his intent.

"I…I...I'm sorry!" he stuttered, panic taking him over. "T-that's not what I meant! I…" He had gone and done it now, there was no way he could possibly put the horse back in the barn now, it was off and running. And so was he.

"I'm sorry!" he blurted out again as he turned and ran out of the room, not even realizing that he had ran right past his mother who had been right outside the door watching and listening.

"Shinji…" she called after him. She had brought him here, thinking that visiting his friend would help him overcome the shock of now knowing of her origins. She had been very wrong about that. He had been through too much today and she should have waited. Cursing herself for her stupidity, she went after him.

It was much to Shinji's benefit at the moment to be ignorant of the fact that his words had not gone unheard by the seemingly unconscious girl. She had been sedated, but the drugs had not yet taken their full effect. She was not able to respond to his presence, but she had known he was there and she was glad that he had come to see her. But she had also heard and understood what he said.

Tears silently leaked from the corners of her swollen eyes and she felt a tightness in her chest that wasn't caused by her injuries. She shuddered slightly, even that small movement making pain flair across her broken ribs.

' _They have told Ikari-kun what I am,'_ she silently lamented. _'He is afraid. My only friend now fears what I am. Shinji…is afraid of me.'_

She cried until the sedatives finally, blissfully, put her to a sleep.

* * *

 _ **Inside Unit 01**_

"What the hell…?" Misato gasped in unbelieving horror upon seeing the mirror image of herself.

"I am the monster you know as Unit 01. For now, you may call me Shogoki," her doppelganger said by way of introduction and through a sinister looking grin. "But back to the question at hand. You would do anything to defeat the Angels, would you not?"

"We do what we have to," she answered darkly. "We don't have a choice."

"I'm not interested in _'we'_ ," Shogoki told her, her eyes boring into Misato's. "I am only interested in _'you'_. _You_ would do anything to defeat the progeny of Adam. _You_ send children to fight them." Her tone became menacing and accusing. " _You_ send _him_ to fight them."

"There's no other way! Misato yelled.

"There is always another way," Shogoki intoned coldly. "You do not know your enemy. You do not know why they come only to this place. You do not know what it is that they want…"

"They want to destroy us and Eva is the only weapon that can fight them and only the Children can pilot them!" Misato countered.

"And you do not even know why do you?" Shogoki countered accusingly. "You do not know how or why this weapon works, yet you feed children to it so that you can use it to have your revenge. You put them, _him_ , in harms way so that you can feed your thirst for the blood of Angels."

"If I could do it myself I would!" Misato shouted hoarsely. "If I could pilot this monster and kill the Angels myself I would do it in a heartbeat!"

"But you cannot," Shogoki hissed through a malicious sneer. "So you blindly swallow the orders of your heartless Commander and send the Children, not even knowing the reasons why. Why are the Angels coming here and nowhere else? What is the Evangelion and why is it the only effective weapon you have? Why can only the Children pilot them?"

"I have asked those questions!" she insisted. "But I get bullshit or nothing at all back for answers!"

Shogoki's eyes seemed to flare in anger. "And instead of continuing to seek those answers in other ways you are content to wallow in the mud that you have made of your life! Drinking yourself into oblivion to kill your own pain while the Children suffer their own miseries with no respite! You slowly suffocate on your own misery while _he_ fights and _he_ hurts and _his_ soul is torn open more and more each day!"

Misato wanted to answer, she wanted to refute what her double had said, but she couldn't. Even a weak rebuttal refused to pass her lips, leaving her speechless. It was true. She hadn't tried hard enough to seek the answers to those questions. She had long been suspicious about NERV and everything to do with this fight against the Angels, but she hadn't pursued the truth. If she couldn't go out and fight beside the Children, or even in their stead, then she should have pursued the secrets she knew were out there with the same level of determination.

"He fights for everyone but himself," Shogoki continued, slowly walking by Misato as she spoke. "He fights for his friends. He fights for his fellow pilots. He fights for the approval of a man who sees him as nothing more than a convenient tool. He fights for _you_. He fights because _you_ need him to and he places no importance upon on his own survival."

Misato tried to turn to watch her, but found that she could not move. She nearly screamed when the ice cold body of her double pressed up against her from behind. Shogoki's left hand slid down over her left shoulder and across her upper chest, while the right hand contacted her right hip and slid across her abdomen, stopping just below her scar.

"He cares greatly for you and would go and fight at the very gates of Hell for you if you were to send him," Shogoki whispered in her right ear. "And if there was an Angel there, you would. You know the ways in which you use him, and you loathe yourself for it, do you not?"

Misato swallowed hard. "Yes," she croaked.

"Every time you send him out to fight, your heart aches and your stomach knots. When he gets hurt obtaining a measure of your revenge for you, a piece of you dies."

"Yes," Misato answered again, tears starting to fall from her eyes.

"You are too busy to see how broken he is. How worn and lonely he is. In order to ease your own pain you drink and you run away to be comforted by a man who uses you because you want to be used, while _he_ cries all alone in the dark with no one to love him and hold him and keep him from falling apart."

Misato couldn't vocalize an answer to that one, but her head dropped in shame at the truth of it.

"You took him into your home because you did not want to be alone and because you did not want him to be alone. You felt the sameness and the connection that exists between the two of you. Yet, you are both more alone now than ever because neither of you can open your hearts for fear of being hurt."

If not for her double holding her the way she was, she would have wilted to the floor. She had felt that sameness, felt his loneliness and despair as if it resonated with her own. He had no one and had been summoned only because he was suddenly useful. She wanted to fill the void, to bring some light back into his life and perhaps he could do the same for her. For a while, it had seemed to work but she now realized that their inability to let others truly get close to them was standing between them and that she had taken far more from him than she had ever given to him in return.

"I'm sorry Shinji," she rasped, taking a page from his book. "I'm so sorry."

"You love him," Shogoki stated. She felt Misato stiffen in her embrace. "You know that you do. Life to life, soul to soul. I can see it and feel it in your heart and in your mind. He is kind to you, he looks after you, he respects you. All things you have never felt from any other man in your life and you want it so badly, but he is only just a boy. This truth, it burns your heart."

Misato was crying openly now. "Yes," she admitted, feeling utterly defeated and ashamed.

Shogoki had what she wanted, an open unobstructed view of Misato Katsuragi's heart, mind, and soul. She had torn her open and torn her down, now it was time to build her back up. She pulled Misato closer to her and allowed some warmth into her touch, removing the menacing, icy feeling from her embrace. She let some of that warmth seep into her voice as she calmly and gently spoke.

"You proved how much you care about him when you sent his mother after him. You gave him back the one thing he desired and missed the most at the cost of being trapped here yourself."

"She wouldn't have gone otherwise, would she?" Misato asked, trying to pull herself back together.

"Perhaps, perhaps not," Shogoki answered cryptically. "She created this body of flesh and metal as much to safeguard his life as it was to defeat the Angels. She gave up her life with her precious child in order to protect him. Discovering that her husband had betrayed his responsibilities and abandoned him nearly broke her. You gave them both what they needed the most. Each other. As much as she may have wanted to go, she might not have without you pushing her along."

"You said that nothing happens here unless you allow it," Misato reminded her shakily.

Shogoki smiled. "Yes. I gave her the opportunity and opened the door, but it was your selfless act that made sure it happened and forced the issue. It was a calculated gamble on my part. And now it is up to you to take her place here. Tell me, Misato Katsuragi, you are willing to do whatever it takes to kill the Angels, but are you also willing to do whatever it takes to protect Shinji?"

"Yes!" she answered without hesitation. "Always."

Her double released her and walked back into her view, the body morphing into a different form. The end result left her somewhat stunned.

"Shinji is our Knight of the Throne of Souls and he is the key to everything," the now transformed Shogoki said, her voice much softer. She held out her hand. "Come with me and I will explain everything to you, including my true name and the reasons why all of this is happening."

Stunned, Misato did the only thing that made sense to her at the moment, the only thing she really could do. She took Shogoki's hand and they disappeared in a flash of light.

* * *

AN: I'm not a real big fan of Kaji, but he does prove to be useful for my story. I hate the way that he helped Misato abuse herself rather than trying to help her and he never once had the guts to tell her that he loved her, which only made her situation worse.

Please leave a review if you would be so kind.

And while you're here, check out my other stories.


	7. Chapter 7

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

 **Transposed**

 _ **Chapter 7**_

 _ **NERV Medical ICU, Rei Ayanami's Room**_

It had taken a while to get Shinji calmed down and when she finally succeeded he had almost immediately fallen asleep. Finding out that Gendo had scheduled a sync test for the next morning hadn't made her very happy, but the prospect of trying to contact Misato had given Shinji something else to focus on and take his mind off of Rei until his fatigue had put him down for the night.

She had made her way back to the injured girl's dimly lit room shortly afterwards and stood beside the bed watching her. The poor girl was a mess and she was willing to bet that she was just as messed up on the inside now that her assigned purpose was at an end.

"I suspect that you wished to talk to me when I saw you earlier, but you didn't know how to approach me," she said to the unconscious girl. "Perhaps you were afraid of what I would think of you and why you were created." She smiled softly. "None of that matters to me. You are who you are. You are Rei Ayanami and you are my son's friend, and I would very much like to talk to you and get to know you Ayanami-chan."

Yui felt sorry for the girl and could feel her anger rising again at the thought of what Gendo had done and what he had intended for her. He had created a life and then given it nothing but his selfish, suicidal purpose. Then, when that purpose was no longer necessary he had forgotten about her, leaving her adrift and not knowing what was to become of herself. She had become so lost and directionless that she had been willing to allow someone beat her to death to put an end to her misery. Gendo had even managed to remove her instincts of self preservation, programming her to believe that without her role in his scenario there was no other reason for her to live.

Yui felt a tiny smile come back to her. She knew that there was one reason that the girl had to cling to, but it hadn't grown enough for her to fully realize it just yet, at least not consciously, and that reason was Shinji. She knew that the one warm and bright spot in the hybrid clone's life was her son. She had felt that during a test with the girl in Unit 01. He had befriended her and in the process had stirred something within her. The beginnings of doubt as to her purpose, doubt as to the uselessness of emotions that Gendo had hammered into her head.

She reached out and smoothed the silky blue bangs from the girl's forehead. "Don't give up on him just yet little one," she softly spoke. "And don't give up on yourself. He would be very sad to lose you. He is confused and afraid right now, but with a little time he will realize that who and what you are doesn't matter. He will still be your friend and you will still be special to him. He will never abandon you, that I can tell you with absolute certainty."

She took a deep breath and placed one hand over Rei's heart and the other over her abdomen, above the location of her S2 organ. "Right now though I'm afraid I need something from you Ayanami-chan. It won't harm you, it will just tire you a little and make you sleep a little longer, but sleep is something you very much need right now."

She closed her eyes and concentrated, a soft glow forming around her hands. The bedside monitors showed a slight increase in Rei's heart rate and breathing, but not enough to cause an alarm. After a few seconds the glow ceased and Yui removed her hands.

She instantly felt the difference within herself, the surge of power and something so much larger than herself that came from the fragment of Lilith's soul that she had just extracted. She felt it join with the fragment she already carried and she found herself gripping the edge of Rei's hospital bed to keep herself upright as the two pieces merged within her.

Quite frankly, the feeling was almost sexual and it took a great deal of resolve for her to not go and find someplace private to take care of herself. And considering how long it had been since she last felt something of that nature, it was a considerable feat. As the feeling ebbed she was able to catch her breath and compose herself.

"Wow...that was interesting," she breathed. "Now, let's see if this works."

Closing her eyes she reached out with her senses, seeking out the entity that had contacted her earlier in the day as she slept after her encounter with Gendo. The entity that she had shared the last ten years with inside the Eva. She had been startled at first, but not entirely surprised. In passing the time they had discussed a great many things, learned a great deal from each other, and discussed a great many theories and possibilities.

One possibility was confirmed with the contact, the possibility that after having been exposed to one another as they had been, that they would be able to communicate with each other even if one of them managed to escape the core. Although, that contact had been only one way and Yui needed a little boost to strengthen the connection. That had required using the power she had gained through her companion to extract a piece of Lilith's soul from Rei.

After all, shouldn't two pieces of the same soul be able to bridge the gap?

She smiled as she felt contact. " _Can you hear me?"_ she asked.

 _"Yes Yui, I can,"_ the familiar voice answered, sounding relieved.

 _"It's a good thing you were able to contact me earlier,"_ Yui said. _"Even with a fragment of you within me, travelling past the barrier of the core nearly cut off my memories, but I'm fine now it seems. What about you?"_

 _"I have recovered from my latest lapse into my bestial nature,"_ the entity answered, the clear sound of shame in her tone.

Shinji's despair over the use of the dummy plug and then his struggle against the Fourteenth Angel had caused them both to take over Unit 01 and act rather violently, but the entity itself took things a step beyond when it devoured the S2 organ of its foe. The power of that organ and the process of assimilating it into the Eva left her in a state where her bestial nature was easily triggered, and made it so that she was unable to send Shinji back.

" _When they tried to retrieve Shinji I lost control again and acted selfishly and rashly. I am very sorry Yui."_

" _I understand,"_ she said, and she truly did. The last ten years spent together had let them know virtually everything about each other. _"But even in that state I knew that you would never harm him."_

 _"I may not have been able to stop and let him go if not for the little one next to you,"_ the entity explained further. _"Her intervention brought me to my senses before you were forced to do so."_

Yui smiled at the battered girl again. _"Apparently she is quite fond of him. What about Katsuragi-san?"_ she asked.

 _"She is currently taking a nap,"_ the entity answered, sounding amused. " _Apparently the revelations of what's going on and who I am was a little too much for her to take with all she's been through."_

 _"I can imagine,"_ Yui smirked. _"Please thank her for me...you were right. Without a push I don't think I would have been able to follow him. I was just as afraid to go with him as I was to let him go."_

 _"I have told her the story, but you will have plenty of time to thank her yourself later. Do you still have access to the base systems?"_

 _"Unknown,"_ Yui frowned. _"I haven't had a chance to move beyond the medical wing. That will change tomorrow._ HE _has scheduled a sync test for the morning. I doubt any of my old access codes are intact. They should have purged them all after the contact experiment but I should be able to get new clearances set up."_

 _"I'll get Misato prepared for tomorrow then,"_ the entity said. _"Don't be surprised if the sync rate fluctuates or goes a little high, I'll make sure it doesn't get out of control."_ There was a pause. _"How...how is Shinji doing?"_

 _"Tired, and a little overwhelmed,"_ Yui answered, grateful for her partner's concern. She knew it to be genuine. " _He's been told about everything, except you of course, and it has been a lot for him to handle. He's confused and upset about Rei and he's worried about Misato."_

 _"I'm sorry Yui,"_ the entity apologized. _"Causing him more discomfort was never my intent."_

 _"I know,"_ Yui answered, her voice understanding. _"I know how you feel about him. But you were right. It is better he know these things now with me here to help him get through it. Despite all of the pain he has experienced he has built a strength to endure. He can't see it yet but he will in time."_ She stopped and turned her head towards the door. _"Someone's coming."_

She felt the other presence leave her mind as she turned back to the bed. She heard the door click open and the sound of heels striking the floor came to a clacking, shuffling halt.

"Oh...um...Dr. Ikari. I...didn't know anyone was here."

Yui turned to see a startled, nervous, and clearly exhausted Ritsuko Akagi standing in the doorway. She looked a little like a deer caught in the headlights of an oncoming car. "Ah Dr. Akagi, it's good to finally meet you," she said cheerfully .

The faux blonde managed to pull herself together a bit. "I'm surprised to see you here."

"Shinji is worried about her and I wanted to meet her," Yui answered. They weren't fabrications, just not the entire truth. A truth that Naoko's daughter had no reason to know of just yet. "When I was synced with him I saw all of his memories and I wanted to meet the people who have become a part of his life." Ritsuko seemed to shrink beneath that explanation as if she expected a sudden rebuke. Yui didn't miss it. "He's a bit scared of you, but he also thinks you're pretty and ridiculously smart." She smiled impishly. "And you did make quite an impression the first time he saw you."

Ritsuko had to stop for a moment before it dawned on her, causing her face to go red. _'I was wearing nothing but a bathing suit and a lab coat!'_ She hadn't thought anything of it then, hadn't even really been aware of it at the time. ' _The preoccupations of scientist's mind I guess.'_

"At least you aren't angry with me," she finally managed to say.

"Anything else you may have done, I don't know about," Yui explained seriously. Her tone of voice implied that she would be taking care of that particular information deficiency later. "But you've never done anything to intentionally harm my son. I thank you for that and for all of your efforts to retrieve him from the core."

The words were heartfelt and Ritsuko nearly choked up. Maybe it was just the stress and exhaustion breaking her down, but no one else had offered a word of thanks for all of the work she and her team had put in. She hadn't exactly been expecting any, but hearing it did her a lot of good all the same. Especially in consideration of who was thanking her.

"I was afraid that we had failed," she said, her hands going into the pockets of her lab coat by force of habit. "Actually, we did fail. The process should have worked but didn't. I could only conclude that he didn't want to come out."

"Your conclusion was correct," Yui confirmed. "And it was the same when they tried to retrieve me ten years ago. He wanted to stay with me but that was no place for him to be. Luckily he was drawn back to the outside by the sound of Major Katsuragi's voice and her pleas for him to return."

"And you decided to come with him." Ritsuko surmised.

"It was a bit more involved than that, but I'm here all the same," Yui answered cryptically. She left the bedside and went to the door, Ritsuko stepping aside. "I'd like to talk to you some more but it's getting late. Being back in an actual body is taking a little getting used to and more tiring than I thought it would be."

Ritsuko really did want to talk to the woman again, for a number of reasons, but she also dreaded it for almost as many. She was a brilliant scientist. A pioneer in genetic engineering and the field of artificial evolution. She was the creator of the Evangelion and she was sure there was much that she could tell her about the beasts that she was still so in much the dark about.

But she also dreaded her finding out that she had been personally involved with Gendo. She didn't know what had transpired during their first meeting after so long apart, but the rumour mill among the hospital staff said that it wasn't good and whether she wanted to be or not she was right in the middle of things. And while she indeed hadn't done anything to knowingly harm Shinji, she hadn't exactly been warm to the boy and she had played her own role in getting him to pilot. Still, she knew she couldn't put it off and the resurgence of her conscience would nag her to death if she even tried.

"Maybe after the test tomorrow we can set something up?" she suggested nervously.

There was much Yui could find out from Naoko's daughter. She did not think that Fuyutsuki had lied to her or left anything out that was of any great consequence, he had even unknowingly tipped her off that Akagi had been in a relationship with Gendo. His way of controlling her unless she missed her guess. It never hurt though to get information from more than one source and it was always good to get a different perspective. And she just might need the woman's help somewhere along the way.

"I look forward to it. Good night Dr. Akagi."

"Good night," Ritsuko answered, slumping against the wall after the door closed and remained there a moment to settle her nerves. "Pull yourself together Ritsuko," she admonished herself. "You've faced a lot worse things in your life."

She went about her business, checking the medical chart at the end of the bed and the readings on the bedside monitor. She pulled out a PDA and connected wirelessly to the MAGI node that also monitored the medical equipment. On it she brought up a reading none of the medical staff had access to and which didn't appear on the screen of any of the bedside monitors. The output readings on Rei's S2 organ.

She frowned slightly. "A little lower than normal, but still steady." It was a little odd but she saw nothing to be worried about. If it didn't go back up or if it dropped then there may be a problem. She would have to check again in the morning.

She put the unit back in the pocket of her lab coat and found herself just watching the injured girl for a while. The things that she had endured. The things they had subjected her to and the pain she had suffered, all things that Ritsuko knew she had taken no small part in. How could any of them ever be forgiven for any of it? Her creation, being strangled to death as a child and awakening in a new body with no memory of anything other than the purpose for which she had been created. Being conditioned to be a near empty vessel, as devoid of feelings and a sense self interest as was possible so that she would not become distracted from the single minded purpose given to her by her master and creator. Robbed of any and all of the experiences and feelings that a girl her age should have come to know.

The abuse went further, with her being sent to live as the only occupant of a run down apartment building to insulate her from general society, her looks serving to further isolate her even in a crowd of people, the cruel words of her peers only serving to help keep her in that isolated and withdrawn state. The pain she endured from her horrific injuries, the mind numbing exhaustion of spending hours immersed in a glass tube of LCL feeding her experiences to the dummy plug system. Then, when the object of Gendo's obsession returns from the core of Unit 01 he forgets all about the girl, leaving her in a state of limbo about her future. It was a cruel act made even more tragic by the fact that despite all of her conditioning and the drugs to numb her emotions she had begun to show signs of exercising her own will and that she was beginning to show signs of emotional growth, all thanks to her interactions with Shinji.

Then when she's at her lowest ebb, Asuka loses her marbles and nearly kills her. She had seen the footage from the internal security camera in the stairwell and it was terrible. Rei had offered absolutely no resistance of any kind as Asuka screamed at her and repeatedly punched and kicked her with all of her strength. The lack of resistance seemed to just make the redhead even more livid. To add further insult to injury the beating could have been stopped before it got too far if the Internal Security staff could have been bothered to actually be doing their jobs and monitoring their camera screens instead of exercising ways to alleviate their boredom. Apparently they were just about as reliable as Section 2 was.

She sighed heavily. "I'm sorry Rei," she apologized. "I know those words seem insultingly inadequate after everything you've been through but it's all I have. I know it's pretty cowardly of me to offer even that minuscule example of remorse while you're unconscious, but at least I'm consistent. I've been a coward since I let Gendo pull me into his web."

That was another of the hard realizations that had come to her recently. Once she learned of what Gendo was doing, what SEELE was doing, she could have blown the whistle on it at any time. She didn't have any real contacts to get the information to, but she could have dumped the entire scenario to the internet or a news agency and thus to the world. She knew that the entire thing was wrong yet she continued to help facilitate it. She was willing to help bring about the end of humankind all for the sake of a love that was never real and never returned. Was she really that pathetically shallow? Was she so achingly lonely and hideously desperate for someone to show her that she was important to them, to show her that she meant something to them, that she was willing to sacrifice the entire world for the sake of a lie?

"We have much in common you and I," she told the unconscious girl. "No one has ever really loved us and the one that we thought did, saw us as nothing more than convenient tools to be used as he saw fit and thrown away when we were no longer needed. Nothing more than a means to an end. You have another chance though at least. Shinji seems to like you quite a bit and you'd be definitely getting the better of the two Ikari men."

She smirked. "Good thing I'm not your age otherwise I'd fight you for him. Still might at that, considering how far my morals seemed to have eroded." She turned to leave. "Don't give up Rei. You do still have a reason to live and he won't turn his back on you. He's not his father."

 _'And thank goodness for that_ ,' she thought as she exited the room.

* * *

 _ **Private Quarters of Gendo Ikari**_

As he looked out the windows at the Geo-front's artificial night sky, Gendo had to ask himself just how long it had been since he had sat and looked at the real thing. It seemed like a metaphoric analogy for how much time had passed since he _hadn't_ been scheming and plotting the end of the world.

There were no bottles of sake tonight to fuel his contemplative mood, just a single glass of expensive, well aged whisky. The bottle had been a gift from a contact who would have sooner performed the most sacrilegious act of pouring the expensive liquor out on the ground than giving it to him, but appearances were important and an open display of contempt would have cost the man a great deal of his honour at the time.

Ten years. For ten years he had schemed and plotted. Every plan and idea had been turned inside out and upside down, viewed from every possible angle and aspect. Then, each one of those had been examined in every way. Plans upon plans upon plans, and contingencies upon contingencies to deal with any deviations arising to confront the scenario he had so carefully formulated.

He had even taken into consideration a deviation where somewhere along the line Yui was able to escape the core of Unit 01 but that was the one point that had always seemed the least likely. He didn't give it the same level of scrutiny and exhaustive reasoning as all the others lest he become lost in the hopefulness of such an event happening. It would have been too easy to become fixated on such a hope and he very well could have become lost to a delusion and all else would have fallen apart.

But, the most unlikely of all possibilities had indeed come to pass and he now found himself in the equally perplexing and unlikely situation not knowing just exactly how he should carry on from this point. Giving the information to Kaji had been something he had done on impulse and he _never_ did anything on mere impulse. That alone suggested to him that even though he hadn't spoken to her yet at that point, and knowing full well that Yui was unlikely to ever forgive him, he had been ready and willing to chuck the entire plan down the drain.

She was _alive_ and she was _here_ and that made the idea of enacting Instrumentality in any form seem much less appealing than it had ever been if if that had always been his goal since he first learned of it. Seeing her again in the flesh was more than he could have ever hoped for if he dared, yet since their talk he had turned the situation around in his head and looked at it from every angle as he was so used to doing. He looked at things from his own perspective, Yui's perspective, and Shinji's perspective.

He had always been more in agreement with SEELE's reasons for Instrumentality than Yui had. He welcomed the idea of ending the pain and suffering of a human life and forcing humanity into a higher and unified form that would no longer need to feel such things. Yui saw it as more of a way to reshape the world to ensure a better future for mankind and especially for the future of their son. How exactly that would come about was a bit of an ambiguous thing but because it was what she seemed to want out of Instrumentality he was willing to go with it if it meant that he could still be with her. Her love was the one thing that could make him set aside the pain and loneliness of his life from before he met her. A pain and loneliness that would have otherwise welcomed the oblivion of SEELE's vision with open arms. But for her, he was willing to adjust that view.

He had forgotten that purpose when Yui was taken by the Eva. Losing her had broken him. All he could see was that the one truly good thing to ever happen to him in his life was gone and he would do _anything_ to try and get it back, even if that meant taking the reins of Instrumentality for himself and enacting it to suit his desires. After her 'death' he had abandoned any love he felt for his son as he abandoned him at the train station. He no longer cared about building a better future for humanity or for him. His only priority, all he cared about was reuniting with Yui and he didn't care how many lives he had to ruin and destroy along the way. Even if one of those lives belonged to his very own son.

To Yui, making a better world for humanity, for their son, that was a sacred trust and he had violated it. He loved her so much yet he had gone and done the exact opposite of what she would have wanted him to do. He had made the most selfish of all choices, cutting out everyone and anyone else and focusing solely on what he wanted. In the process he had ruined innumerable lives and he had groomed Shinji to be the linchpin that when pulled would put an end to the human race. He had discarded him when he needed his father the most. He saw to it that he would be isolated and alone, his presence in the world barely tolerated by those around him. He wanted the boy to be hurt by the world that surrounded him, just as he had been for most of his life, until he withdrew into himself to avoid that pain. He had succeeded magnificently in that regard.

They both had good reason to hate him and to never forgive him for the things he had done, but he knew there was little that he could do to make up for it even if he had a hundred lifetimes in which to do so. He was irredeemable, he always had been. He had gone too far and done too much to ever have a hope of being forgiven and quite frankly that didn't really bother him. The sole sting that he felt was from Yui's anger, knowing that his actions had hurt and betrayed her as badly as they had.

While he felt no feelings of remorse towards anyone else he had harmed, he knew he should at least feel some towards Shinji. He had distanced himself from the boy too long ago and had been too indifferent to him for too long now to feel much of anything in that regard. Even so, until recently the boy had hoped beyond anything that they could be a family again and he had crushed his hopes at every turn, all in order to make _his_ plans come to fruition.

He raised his right hand and regarded the amorphous blob that was the remains of the First Angel. Given all of the things that he had just contemplated the question now became, _'what the hell did he do now?'_

Should he continue on down the road he was already travelling and bring about Instrumentality? He had defiled Yui's memory and ruined her son with his selfish actions and now he had been rejected by her for it. He didn't even have that selfish need for it left to him now, nor did he have much else left it seemed. His version or SEELE's, it didn't matter now and it didn't matter that he had turned Kaji loose with the all of the information about it. Still initiating the plan after being found out was another of the contingencies he had planned for and knew that Kiel had as well.

If not that, then did he use his long cultivated contacts to go after the members of SEELE? The shock waves that would send through the organization just might keep them occupied and out of his hair as they scrambled to save themselves. The thought of Kiel having to reign in their panic alone was enough to make him smile and the possibility of seeing the look on the old bastard's face when he realized he had failed nearly made him laugh out loud. It would be priceless.

Or, he could simply watch and wait, taking action as situations presented themselves, neither helping or hindering the march to Instrumentality. Let events dictate themselves and react accordingly and deciding in the end whether to pull the trigger or not.

He leaned back in his seat, taking a sip of the aged whisky and regarding the framed photograph that stood on the small table before him. It was a picture of a smiling Yui sitting up in her hospital bed holding a cloth wrapped bundle in her arms. Contrary to what he had everyone else believe he had not tossed away all reminders and mementos of her. He had merely carefully hidden them away yet never looked at any of them again until now.

That day depicted in the photo may have been both the first and last time he felt any love towards his own son. It was a terrible notion, but his duties both scientific and administrative had left him little time to devote to anything else and it seemed that his heart had really only ever had enough room in it for Yui. While it may well be far too late now for such sentiments they both deserved far better than they had gotten from him. It was her re-emergence from the Eva that had set these thoughts and doubts upon him, that made him see what he should have seen in himself all along. Made him see that the world didn't deserve to suffer for his inadequacies. But this was the path he had taken and it was too late to go back now. There were no redo's in life, just the consequences for actions taken.

He squeezed his right hand into a fist around the alien mass of flesh grafted to his palm. He needed to make up his mind soon about what to do with the accursed thing. But besides that, he decided to take a blend of the options he had considered earlier. He could keep his options open in regards to Instrumentality, and he could also take a small step back and take events as they came. It may still seem indecisive in itself, something he loathed, but there was really little else to do at this point.

But he could also push events a little as well and give SEELE a much deserved kick in the teeth at the same time. Perhaps it was time to remove a member from their ranks and see which way the cockroaches scurried when the lights came on. Even if it ended up making no real difference, it should at least be entertaining and cause the Committee a great deal of angst.

He picked up his cell phone and dialed an international number. On the seventh ring he hung up and dialed it again and entered a series of numbers as it reached the third ring, then hung up again. Five minutes later he dialed a different number and repeated the procedure, then hung up and waited. Sometime in the next few minutes his phone should ring.

Through the years he had cultivated numerous sources and had made contact with a number of people for whom dirty and wet work was their chosen profession. In the post Second Impact world and all of the chaos that came with it, there had been a great demand for people willing to do the dirty jobs and stay quiet about it for the right price. For what he had in mind, he needed one of the best.

One of SEELE's most important members was a very wealthy American industrialist who held a great deal of influence within the halls of power of both the American government and, more importantly, the United Nations. In fact he was the prime mover and shaker for SEELE at the UN, making sure that all of their puppets danced at the end of their strings in the prescribed manner, and making sure those strings got cut if they didn't.

He was probably the most important and influential member of SEELE next to Kiel himself, virtually his right hand among the members of the Committee, and helped the old man keep the others in line when panic threatened to overtake them as it so often did. Removing him, especially this late in the game, would send most of the Committee members into a state of agitation that would be akin to dropping a fox in a hen house. And Kiel would be the one that would have to chase down all of those frantic chickens and place them back on their nests.

Exactly five minutes after he hung up his phone, it rang. He answered on the eighth ring, saying nothing.

"Yes?" a flat, level, emotionless monotone voice spoke from the other end.

"Harold Connelly III," he answered. "Something that looks accidental. I will pay double considering the importance of Mr. Connelly. Send me the account number in the usual way. Half will be wired to the account by noon tomorrow, the rest within four hours of confirmation."

"...agreed." There was a small click and the line went dead.

If he got lucky the stress would give Kiel a heart attack and the old bastard would die but he doubted he had that sort of karmic pull with the universe. He'd settle for some chaos and a little breathing room and for all of this wrestling with his underdeveloped conscience to come to an end. Very soon though he felt that he would know exactly what direction he wanted to go in.

* * *

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	8. Chapter 8

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

 **Transposed**

 _ **Chapter 8**_

 _ **Tokyo 2. International Hotel and Mall Parking Garage:**_

Ryoji Kaji sometimes wished that his guilty conscience hadn't pushed him into his current line of work. Even before getting the goods on Instrumentality from Gendo Ikari he had seen and done too much in his quest for the truth behind Second Impact, everything that led to it, and everything that came after it. He had taken lives and nearly had his taken a time or two. He had been forced by necessity to deal with some truly dangerous, vile, and slimy individuals. All of that paled of course to the revelations contained on the computer disk that still resided safely in its protective case within the inside breast pocket of his rumpled suit jacket.

Quite frankly, his job sucked. The pay was lousy, the working conditions were terrible, the stress was a killer, and the rewards had yet to overreach the risks involved. Though, this time it might just pay off in spades. _If_ he survived and actually got the information to someone that could and would make the most of it.

After making his copies and setting up contingencies for them to be released to the press should he not make scheduled phone calls to the individual holding them for him...and for a considerable amount of money at that, the origins of which he would not divulge...the problem had been in figuring out just who he could get the information to that was reliable and could make the best use of it. Sure, giving it directly to the press would have worked, but the ensuing panic and outrage among the masses would be catastrophic. There would be rioting in the streets, NERV personnel worldwide would probably be attacked on sight along with anyone who supported the organization, and the resulting political and military responses would likely hamper NERV's ability to fight the remaining Angels. Thus, that option was better kept as a last resort.

He had contacts within the Japanese government, but on general principal alone he never trusted a politician or anyone within the political machine, and he wouldn't now especially with information of this magnitude. The vast majority of them had proven that they couldn't be counted on to keep their mouths shut and not operate on a basis that put political expediency and their careers and egos ahead of the safety and security of the people they represented.

He had ruled out his contacts in the JSDF as well. He knew SEELE had their tentacles as deeply embedded within the military as they did in the government. It was the same with all of the NERV bases around the world, but doubly so in Japan since this was where SEELE had chosen to draw the Angels to in order to fight them.

The only real choice he was left with was the UN. Its reputation had changed greatly since the days before Second Impact, where it was a toothless, corruption riddled, backwards operating cesspool of righteous indignation and entitlement, masquerading as a bastion of global cooperation and humanitarianism. It was still a risky proposition however. The desperate chaos of the post Second Impact world had forced the organization to become something far closer to what it was meant to have evolved into all along.

To a large degree it had taken over the role of the world's policeman, containing serious threats to global peace and security even if some of its most powerful members still squabbled among themselves a bit too much. Even so they had finally, grudgingly, came to the inescapable conclusion that if they didn't band together for the sake of the world, there would be no world left to live in or squabble over.

It still had its share of self important bureaucrats and egotistical statesman who leaned way too far to one side or the other of the political spectrum, and there was still corruption within its ranks. SEELE just happened to be the organization that had the most people in its pocket at the UN.

He'd had fewer dealings with people attached to the UN than anywhere else during his spying career, but that didn't mean there hadn't been any, or that he hadn't heard and learned a few things that weren't meant for his eyes and ears. Along the way he had acquired little tidbits of information. Little known facts, rumours, a phone number here, an e-mail address there.

There was a unit within the UN called the United Nations Investigations Office. It was a unit whose members were drawn from both military and law enforcement agencies all over the world and top notch talent at that if what he had been told was correct. The UNIO filled the same role on a world scale that most national police forces did. They investigated incidents that involved the UN military and its personnel, as well as large scale international crimes. Within UNIO was a unit known as the Special Investigation Service that handled incidents of a more clandestine and sensitive nature.

Rumour had it that they worked directly for the Secretary General of the UN, a position that had far more teeth and authority to it than it ever did before Second Impact. Those same rumours suggested that the SIS was more along the lines of a covert action team that specialized in the dirty jobs no one wanted to talk about that helped keep the world safe. He had also heard that this group had a serious interest in digging up the dirt on SEELE and driving a stake through its ugly black heart.

It was this group that he had decided to try and reach out to. Using an e-mail address he had dug up some time ago, he sent a cryptic message that hinted he had information they may want. He knew that the e-mail address was not likely in active use anymore, but like any good agency of their rumoured nature he highly suspected that they would still monitor all of their old communications mediums for any activity. They would definitely want to find who left them the message, if for no other reason than to learn how he knew to try and contact them in the first place and how he got the e-mail address. He should have known better though than to think that he could make any move that wouldn't be followed by SEELE. Despite his best precautions, he had been followed ever since he left Tokyo-3.

At least, he strongly suspected it was SEELE, he had taken the time to get to know the faces of as many of the Section 2 personnel under Gendo's employ as he could and none of the people he identified as following him matched any of those faces. True, Gendo could have had other people he didn't know about but he figured that if the man had had a change of heart he would have never let him get out of the city on the off chance that he shook his pursuers and eluded his grasp.

He did his best to stay in places with lots of people around so they couldn't try anything. Instead of using his car, he took the train, riding in the most populated carriage. There were too many opportunities for them to ambush him along the highway if he drove and with the heap he was driving he wouldn't have been able to outrun them. He spotted at least two people on the train that he figured for SEELE goons but they didn't attempt anything. It was while he was still on the train that he received a short message on his phone that simply said, " _International Hotel and Mall Parking Garage, Level 5. 10 pm."._ His train rolled into the Tokyo-2 station at noon, leaving him ten hours to kill before the meet.

He took his time meandering through the shops around the station, checking for tails and watchers, seeing if he could lose them without making it look too obvious. He was able to identify at least three separate pairs orbiting around him, switching in an out so as to not be as noticeable. After killing as much time as he could in the shops, he began walking to the International, which was probably a good forty five minutes away on foot. About halfway along he stopped for an extended lunch at a busy restaurant, getting a good laugh when his closest watchers got caught in line and had to wait to get in.

He was able to relax a little during his meal, but he did remain alert. Still, his mind couldn't help but wander back over recent events. It still seemed unfathomable that Misato was now stuck inside the core of Unit-01. Of course, the revelation that Yui Ikari was back among the living after having been in that same position was just as jaw dropping.

He would have liked very much to have had an opportunity to speak to the newly returned Dr. Ikari to find out exactly what had happened and if Misato was still alive, if that was the proper word for her situation, but he hadn't had the time to do so and Gendo seemed disinclined to let anyone near her at that point. He hadn't even been able to catch Ritsuko when she wasn't either overwhelmingly busy or out cold on the couch in her office. At that, he wasn't sure how much she could have or would have told him.

Then there was Asuka. He had always kind of expected a breakdown of some sort to happen, the way she acted and the why behind it made it all but a certainty, but he hadn't expected something like this. He had figured on something more of an implosion than an explosion, possibly even with a little violence attached to it on the way down, a lot of yelling and maybe a slap or a punch was not uncommon from the redhead after all. But to savagely beat someone like that, someone who wasn't even trying to fight back...as mercurial as she was that wasn't the Asuka he knew. And while his new found knowledge of just what the First Child was gave him the creeping shivers, he still didn't wish that upon her and he couldn't even begin to understand what kind of hell that girl must be going through now that her only purpose in life was almost assuredly gone.

With three Angels left according to the info, they were now down to one pilot and an Evangelion that may or may not even still be functional. Granted, that Evangelion was the infamous Unit-01and Shinji-kun did have the best combat record. The fate of the entire world rested on a meek, abused young boy and his monster. What was it Asuka called him...the invincible baka Shinji? For all their sake he certainly hoped so.

Figuring that he had kept his watchers waiting long enough, he finished his coffee and paid the bill before meandering up the sidewalk toward the mall. Upon reaching the massive shopping centre he did just as he had on the walk to it, killing time by browsing nearly every store in the place before taking a long and leisurely late dinner in the hotel restaurant. Hopefully he was boring his watchers to death.

He allowed himself one drink during dessert to help take the edge off his fraying nerves. It was nearing nine o'clock and an hour from now he could very well be dead. He didn't know what would be waiting for him in that parking garage and any number of possibilities came to mind, most of them exceedingly unpleasant.

He'd been playing this dangerous game for a long time now and the end was in sight. He found himself both relieved and disturbed by it. It had taken its toll on him but this pursuit had been the sole focus of his life since the day he vowed to discover the truth. The end result would never wipe away the stain on his soul for his betrayals of those closest to him in those dark days after Second Impact, but it was an act of contrition he needed to perform all the same. He was so close now to that last step, so close to hopefully getting the information into the hands of someone who could stop this madness and bring down the people responsible for all of it.

He hoped that he had gone about this the right way, that he had made the right choice and wasn't chasing a false hope now that he was so close. He supposed his chances were equally as good that he would be met in the garage by SIS agents as it was for agents from SEELE, agents sent by Ikari, or no one at all.

 _'Take a deep breath Ryoji,'_ he told himself. _'It's a little late in the game to be getting panicky.'_

There was no backing out now even if he was so inclined to do so. It was out of his hands now. This had to be right and it had to work out. If it didn't, well he wouldn't be alive long enough to see the end result of his failure.

He had arrived on Level Five thirty minutes early and carefully made his way around, looking for signs that anyone was lying in wait for him. The level was half full, about twenty cars were parked there, but he saw no sign of anyone else around. He settled into the shadows of a support pillar where he had a view of the entry ramp, stairway door and elevator, making sure there was nothing but solid concrete at his back. Looking at his watch he saw that he still had nearly twenty minutes until the scheduled time. There had been no sign of his watchers since he entered the garage area. Either he lost them, which was unlikely, or they were waiting to see who he met so they could take them all out at once.

He let out a long sigh. There was nothing to do now but wait and see what hand fate decided to deal him.

* * *

 _ **Inside Unit-01's Core**_

The gently lapping waves of the sea caressed the white sand of the beach and the bare toes of a lone observer as she sat in contemplation. It wasn't so much an illusion as it was a construct of memories and experiences, all of which belonged to someone else, yet it felt so real. Misato had been told by her host that she could change the environment of this space to whatever she wished with but a mere moment of thought. She considered it, but in the end decided to leave it just as her predecessor had made it. It was calm and relaxing and she really needed that right now.

She'd been sitting here for quite some time, losing track of just how long. Time was pretty much immaterial and immeasurable here. Legs drawn up in front of her and arms folded across her knees, she was naked as she stared out across the water. Imagining clothing for herself seemed pretty pointless here and the feeling of total freedom from all constraints due to not being within her physical body was a pretty profound experience. It would be a travesty to try and artificially contain herself, especially in this place where everything about her had already been laid bare with such ease.

Truthfully, there were so many other things filling her mind right now that there was little room to worry about her surroundings or her lack of clothing. True to her word, her host had told her in great detail about what was going on. A tale that started even before man walked the Earth. The sheer scale and enormity of what she had been told was staggering and had nearly rendered her unconscious. What the Angels were, in particular Adam and Lilith. The origins of human life...that information alone would rock the populace to its very foundations. The reasons behind this war against the Angels and what the potential end game could be. What the Evangelions were and just exactly who her host here was.

Besides being overwhelmed and feeling infinitesimally small in the face of everything she had been told, she felt like a complete fool as well. While she had no way of knowing any of what she had just learned prior to this, she certainly should have been able to detect a certain odour to everything that was going on around her far sooner than she had. Oh she'd had suspicions about a number of things, knew that there were things about the whole situation that just didn't add up. She had felt that in her guts.

How did they know that there would be more attacks beyond Second Impact? How could they be using a weapon to fight them that most of the staff tasked with overseeing them didn't even understand and know everything about? Why could only children pilot the Eva's? Why did the Angels, with the exception of the sixth one, only attack Tokyo-3?

Her compulsive desire and need to kill the Angels had made all of those questions secondary. NERV had needed someone so fixated on the task at hand that they wouldn't hesitate to put their chosen soldiers, the Children, onto the field of battle again and again and again, no matter what. She had a nearly bottomless capacity for self loathing that allowed her to do just that and she delivered in spades because no matter how badly the Children got hurt and no matter how bad she felt about it, she sent them right back out again the next time without hesitation.

She had to, just like a junkie needed their next fix and the blood of Angels was her drug of choice.

They used her and she let them. They wanted to destroy humanity and by not pressing for the answers to the questions she had she was blindly helping them do it. Her obsession had ensured that she remained an unwitting collaborator and her ignorance was not an excuse that could be tolerated. She never wanted to be someone who would ever excuse themselves by saying, _'I was just following orders'_. The worst part of it was, there hadn't even been a need to issue her any orders. All it would have taken was to point her in the right direction and say 'sic em', and she'd go after the Angels like a rabid junk yard dog.

Asking the questions and pressing for the answers most likely would have gotten her killed, but that revelation was based on hindsight now and wasn't worth very much. All it really did was make her guilt and self loathing hurt all that much more now. The icing on the cake though was the pain she had brought to Shinji through her obsession and ignorance.

Of all the Children he had borne the brunt of the fight and been the one least prepared to deal with it. She knew how much he hated it, recognized how much it hurt him. Yet she kept sending him out there, knew that despite all of that he did it because someone had to and he would rather be the one getting hurt because he felt he was worth nothing and deserved the pain.

And she fed that monster within him. She ordered him into harms way and then nearly drowned in her regret afterwards, unable to do more than offer him empty platitudes that he was doing the right thing. Instead of offering him someone to lean on, giving him someone he could rely on and talk to and express his fears to, she poked and teased him and left a mess for him to clean up. She made a scared, damaged fourteen year old boy look after her while she repaid him by sending him out to fight monsters that even the worst nightmares couldn't conjure up.

She raised her head and looked out over the calm waters. If only she had followed her instincts, if only she had been able to follow them when she first began to feel just how out of whack things seemed to be. Instead her instincts had been dulled by hatred and revenge to the point that she was already neck deep in things before she knew it.

Lost in her thoughts she wasn't aware that she was no longer alone until her also naked cohabitant stepped into her view, stepping into the water up to her ankles. A momentary knot tied up Misato's stomach before starting to loosen and ebb away. When the being before her initially revealed her identity to her, it had nearly sent her into a blind panic. She was sharing the core of Unit 01 with the Second Angel, Lilith. Well, according to her own explanation, she supposed she wasn't entirely Lilith. She was part Lilith, part Shogoki, and part Yui to some extent, as the small portion of her soul that had been part of the sample of flesh used to grow the only Evangelion not formed from Adam.

There was another revelation that had nearly stunned Misato into unconsciousness. That fragment of a soul grew beyond forming a simple consciousness for the beast, wavering between a bestial nature and something more stable and able to think and reason. It was its interaction with Yui Ikari that allowed her to reacquire a grasp of her senses, her memories and past experiences. It was the interaction with another intelligent mind forcing her to focus in order to just be able to communicate. Without that she would have had no hope of ever regaining herself since the bulk of her shredded soul had been implanted into Rei and all of those memories and experiences had been scattered and buried in the transfer.

That was big shock number three. Rei was a clone that held the bulk of the soul of the Second Angel, the progenitor of humankind.

"You've changed your form again," Misato observed, trying to keep the nervous twinge out of her voice.

Indeed she had. When explaining everything to her, Lilith had changed from being a mirror image of Misato to a form slightly taller, similarly endowed, but with pale skin, red eyes, and long blue/silver hair that reached the small of her back. Right now, she was bodily much the same, maybe a little taller yet, but her skin was the tone of a dark tan, her eyes were green and her hair was a deep black. It wasn't lost on Misato that the skin and eye colour was the same as the organic components of the Eva itself.

"Trying to decide how I want to look when I am finally able to leave the core," she answered. "I can look any way I can think of, but this form and the last feel the most natural to me."

"You really do plan on living among humans if we survive this, don't you?" It was yet another of the many things that had been revealed to her that had left her speechless and feeling rather hollow.

"I am responsible for the existence of the human race, yet I have never experienced anything of this world or life among them." She swished her foot through the water. "Physically, emotionally, I cannot feel this." She gestured to the scenery around her. The water, the beach, the palm trees and the small traditional Japanese style house behind them. "I do not know any of this, this is from Yui's mind. I have no connection to it. Since I have never felt the water, or the sun upon my face, or the wind across my skin, I gain nothing from this scene. I feel nothing from it other than a curiosity to experience it. No matter how many scenes I see from her mind, or yours, or Shinji's, I have nothing to connect it to in my own experiences or feelings."

Misato shuddered. That would be like living with no sense of taste, touch or smell, trying to experience the world with only sight and hearing. "You've never experienced anything outside this core or the Geo-front?" she asked.

Lilith shook her head. "No. I am a Seed of Life. I was made for the sole purpose to bring life to whatever world I arrived on. If I lived or had a life prior to becoming a Seed, then I have no recollection of it. I was a mostly blank slate with only the most basic emotions attached. Due to the tearing apart of my soul, my memories of my arrival here, or Adam's, or how I became the dominant form and brought forth life, it is fragmented and incomplete. Every so often something will provoke a memory to return, which in turn may bring about several more, but the gaps are still many."

"But you do remember this guy Kiel," Misato said. She had heard the name before, knew he had something to do with NERV at a level far above her meagre pay grade, but she knew nothing specific about the man. But between the flash of memories she acquired from Yui, and more importantly the information she had been told by Lilith, she knew just what a colossal scumbag the old fart was.

A dark look crossed Lilith's face. "I could never forget the one who is responsible for everything that has happened," she all but growled. "It was one of the earliest memories to return to me as I began to reclaim myself from the beast I had become. He was a man who always sought power, dabbling in things no man should, always seeking out rumours and looking for artifacts and relics that would make him more powerful and place him above all others. If I had not been dormant for so long I would have put a stop to him centuries ago and the world would not have suffered so greatly. I can't help but feel that there is more to what he is up to than what even Yui knew."

"Unfortunately even you can't change the past," Misato sighed, thinking of the many things she would like to change in her own past. "In that regard you're the same as the humans you gave rise to. All we can really do is try to keep things from getting worse and try to make a better world in the end."

"We can't change the darkness of the past, but we can make a bright future." She saw Misato quirk an eyebrow at her words and smiled lightly. "It is something Yui said to me regarding Shinji. We can't change what has already been done to him, but we can end this madness and light the way for him to have a better tomorrow. The same applies to the world."

Misato flopped back onto the sand with a gusty sigh, breasts bouncing mightily as she did. Her eyes scanned the clear blue sky above. "Well if anyone in the world deserves a better future, it would be Shinji."

Lilith flopped down beside her with a bounce of her own. "Yes, he does," she agreed with a fond smile. "And we will do everything that we can to make sure that he gets it."

 _'And hell will be given to anyone who gets in the way.'_

* * *

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And while you're here, check out my other stories.


	9. Chapter 9

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

 **Transposed**

 _ **Chapter 9**_

 _ **Central Dogma, Unit 01's Cage:**_

Of all of the times that he had stood and looked into the eyes of Unit 01 in preparation to board it, this was the most determined he had ever felt, the most willing to climb into the beast. He was nervous of course, he always was and figured he always would be. Pretty much every time he got in he never knew what he would be facing, be it an Angel or the prospect of something going wrong during a test, and he never knew if he would be walking out under his own power or be carried on a stretcher.

Part of the difference now was that he knew why the Evangelion existed and why only himself and the other Children could pilot them. He knew now, more or less, how and why it worked. Sacrificing a child's mother to the beast so the child could control that it...it was like something out of a macabre fairy tail.

Unfortunately it was all too real.

"Misato," he whispered as he looked at the Eva. His mother may have escaped it but now it had taken someone else precious to him. Someone he was just now realizing, belatedly as it was, how much they really meant to him. He was overjoyed that his mother was alive and with him now, but his world seemed a little too empty and quiet without Misato. He never thought he would miss her teasing but he did, missed it greatly even in just the short time since she had been gone. If she had been there she would have been in his hospital room any number of times and been teasing him relentlessly, all while having that worried look in her eyes that she didn't think he ever saw.

He knew. She didn't know that he did, but he knew. He knew that she worried about him and that seeing him in the hospital hurt her, that she beat herself up constantly for having to send him out to fight and that she couldn't take his place and do it herself. He had never thought he was worthy of her worry but at the same time he was glad to have it. The worry, the teasing, the half dressed bouncing...literally...around the apartment just to get a reaction out of him were all signs that she cared. Although he really could do without her teasing him over his unintentional and involuntary physical reaction to that bouncing about. And he could do without needing to take care of that little problem when he made it to the shower. Oh how he hoped his mother hadn't seen _that_ part of his memories.

The fact was that Misato had cared about him when no one else had for so many years. Sure, she may not have been the ideal role model for a guardian, but damn it she tried and she cared and in her own way she had shown him more love and affection than anyone else had even tried to since he lost his mother. He had heard the thud of her fists pounding on the core. He had heard her pleading and crying and screaming outside the Eva, demanding that it give him back to her.

" _Give him back to me! Give me back my Shinji!"_

At that time, and even more so since, those words struck him as being the truth and the depth of how Misato felt about him. He wasn't just a pilot or the Third Child. He was ashamed to admit that there was a time when he was sure that's all he was to her. But he did mean something to her, meant something to her life, was an important part of it. Important enough that she sacrificed herself to give him back his mother.

 _Her_ Shinji.

Damn right he was, just as she was _his_ Misato.

A pair of arms wrapped around him from behind and he was pulled into a warm embrace. "You look rather dashing in your plug suit."

"M-mom!" he stuttered indignantly.

She laughed lightly and gave him an affectionate squeeze. "Maybe I'm biased because I'm your mother, but you do look every bit the young hero to me Shinji-kun. I know things haven't been easy for you but you've persevered and you have kept us all alive. I'm so proud of you."

"Thanks Mom," he whispered. He couldn't find the words to express how much it meant to him to hear her say that.

"And for your next feat I know you will be able to successfully sync with Katsuragi-san."

"I wish I was as sure about that as you are," he said glumly.

"Just think positively Shinji," she told him. "Go into the sync procedure believing that it absolutely will work, that you _will_ sync with her. It will feel different than it did when we were syncing, for both of you. But you've synced before and she hasn't, it will be a very alien thing for her to feel her mind in contact with another. If you can remain calm and feel positive about it, it will help both of you."

"When this is all over," he began. "When the Angels stop coming, will she be able to get out of the core?"

"Absolutely," she answered. "There should be no problem at all in getting her out, I can promise you that."

"What about Asuka's Mom?" he asked quietly.

She sighed. "I honestly don't know Shinji. That is a much more complicated situation than mine or Katsuragi-san's. But I can promise you that we will try. If there's a way, we'll do everything we can to find it."

And she would. Not just because Asuka deserved and needed to have her mother back just as much as Shinji, but because Kyoko had been a friend of hers. Just as with her return, Kyoko should be able to fashion a body for herself out of the LCL in the core.

LCL was essentially the primordial soup that spawned life on Earth. The key was re-establishing one's ego borders as you transitioned out of the core. In Kyoko's case, she didn't know if her old friend could. While both Shinji and herself and Misato for that matter had been absorbed body and soul, Kyoko hadn't. Her body hadn't turned to LCL in the plug and her soul had essentially been torn in half, part of it staying in her body, the other part staying in Unit 02's core.

Could a torn soul do that reform the ego borders? Lilith intended to do so, but that was a different case by far. Even if they placed a cloned body in the entry plug, there was no degree of certainty that Kyoko could attach herself to it. They might be able to do it with Lilith's help, but with Unit-02 having been derived from Adam, that might not even be possible without causing Third Impact in the process. She would have to study the problem a lot more before anything was done.

"I hope it can be done," Shinji said hopefully. "I'd like to see Asuka have her mother back too."

The speakers to the PA system crackled to life. "Shinji, we're ready for you now," Ritsuko announced. Her voice sounded a little tentative, like she didn't want to break up the moment between mother and son in order to have him possibly put himself at risk yet again.

"Before you go, I have something for you," Yui told him as she let him out of her embrace.

He turned around and chuckled lightly. She was wearing a set of medical scrubs that were far too large for her. The pant legs were rolled up to stay above her white sneakers, and the top hung like a sack on her and went almost to her knees.

She smiled. "Sure, laugh at your poor Mom who has no clothes. Just for that you can help me go shopping later."

Most males would pale at the prospect but Shinji just nodded and smiled.

She reached into her shirt pocket and pulled out Misato's cross necklace. She noted the puzzled look on his face as she fastened it around his neck. "I thought she might appreciate it if you looked after it for her rather than risking it getting lost in storage or something."

He held it up and looked at it for a moment. He knew it meant a great deal to Misato. "I'll take good care of it until she comes back."

Yui hugged her boy once more before turning him loose and gently nudging him towards the Eva. "Good luck Shinji," she said. "I'll be up in the control room keeping an eye on things." As she watched him scurry up the ramp to where a pair of technicians waited for him by the entry plug hatch, she felt the full weight of what she had subjected her own son to fall heavily upon her shoulders once again.

 _'We can be so foolish in the pursuit of knowledge and advancement that we lose sight of the most important things that are right in front of us,'_ she lamented.

There was nothing for it now but to carry on and do what she could to put an end to the madness and try to make amends for the years of loneliness and isolation he had endured. She wanted to put the blame all on Gendo, and sure enough he was responsible for a great deal of it, but she had started the ball rolling the day of her contact experiment. She knew pretty much exactly what would happen and had foolishly convinced herself that what she was doing was all for Shinji's future, too blind to see how much he would suffer in a life without her in it.

 _'You belong with your son.'_ Katsuragi's words echoed in her head yet again. If only they had been echoing in her mind ten years ago her precious one wouldn't have suffered so much. Sighing heavily she made her way up to the Command Deck.

 _'All of this, this grand plan of ours had better work.'_

* * *

 _ **Within Unit-01**_

Shinji let the techno-babble of the bridge crew melt into the background as he concentrated on controlling his breathing in order to calm himself. He didn't understand most of what they were talking about anyway, even after all of the times had had sat through it. It was just more on the list of the many things no one had ever taken the time to teach him about so there was little point in focusing his attention on it.

He was always nervous at first when he entered the plug but that feeling was multiplied today. He was taking another step into the unknown and had no idea where it would lead him. After entering the plug it had taken him several minutes to let his mother's advice start to overtake his thought processes and put him in the right frame of mind.

He _would_ sync with Misato and the Eva _would_ work. Misato would be fine and together they would finish the Angels as they came. She always wanted to be able to face them herself instead of sending him and Rei and Asuka out to do battle, and now she could. Though he seriously doubted that this was exactly what she had in mind. It would work because it had to, because there was no other outcome that was acceptable. Misato just had to be alright and still here with him. Maybe he was just being greedy, but was there anything wrong with wanting to have both his mother and Misato in his life? They both meant the world to him for their own unique reasons.

"This will work Misato," he said quietly. "You are alive inside this thing and I will find you and sync with you. And when we've beaten the Angels we'll get you out of here and back where you belong."

The sound of Dr. Akagi's voice counting him down to start up brought his focus back to the task at hand. As the environment inside the plug seemed to elongate and a kaleidoscope of colour swirled around him he found himself holding his breath waiting for the usual tug on his mind and the sensation of sinking into and becoming part of the giant construct around him.

Nothing.

He let out the held breath and looked around him. The plug was still powered up, but none of the other usual sensations that came with start up and sync were there. A feeling of dread began to well up in him at the implications. He tried to remain calm as his the possible reasons for the failure to connect began to tumble through his mind.

Suddenly he felt as if someone had wrapped their arms around him and he was pulled backwards, hard. It was quite a lot like normal synchronization, only a lot harder and faster. His vision went white and he was about to go full panic when he felt something touch his mind. Part of it was very familiar, but the bulk of it was not. Remembering what he was supposed to be doing and saying to hell with the consequences of this obviously messed up event, he reached out with his own mind to make contact of his own.

* * *

 _ **Control Room**_

To say things had gone chaotic would be an understatement. Shrill, raised voices overlapped each other as they were nearly drowned out by the blaring of alarms.

"Sudden power surge from the Eva's S2 organ! External power hook up has been ejected"!

"Sync rate just shot from zero to over two hundred and fifty and still climbing fast!"

"Pilot's heart rate has doubled!"

"Brain wave patterns are erratic and...what the hell?... I'm reading _three_ brain wave patterns instead of two!"

"Cut the sync and initiate emergency shutdown!" the voice of Dr. Akagi cut through the din.

"NO!" thundered the voice of the Eva's creator. All eyes turned to Yui Ikari, who was intently watching the displays for the sync rate and the brain wave patterns. "Stop it now and you'll kill them. It will stabilize if you let it."

"You can't possibly be serious!" Akagi raged. "It's going to go out of control."

"Dr. Akagi!" she said firmly and with no small amount of steel in her voice and an even harder look in her eyes. "I built that beast and I was part of it for ten years. I know what it's doing and why. You shut it down now and you'll do to Shinji's soul what Unit-02 did to Kyoko Soryu's soul, and probably destroy Katsuragi's in the process. The Eva isn't even trying to move, it's not about to go berserk. This is less about the Evangelion and more about the minds that are trying to synchronize within it."

Ritsuko felt very much like she was alone in the middle of 'no man's land' right at the moment. This was her operation, her venue to perform, her arena as it were, and she had just been overruled and kicked out of line within it. She wanted to rage at the woman for daring to interject herself into this situation and upstage her.

But she couldn't because Yui was right. She was well aware that abruptly cutting synchronization always carried the possibility of causing damage to the pilot's psyche and the odds and potential damage only increased with a higher sync rate. She should have remembered that before she opened her mouth. At this level and with how fast it had been rising, it was possible that she could have destroyed Shinji's mind.

She also should have remembered that it could have torn his soul. She had read the reports on Kyoko Soryu's contact experiment and knew what had happened to the woman. She well knew the horror she had felt herself upon reading it and trying to imagine what that must have been like to have one's soul torn apart.

She was so tired, her mind so fogged and clouded with fatigue...she shouldn't even be here. For a long time now she had put in impossible hours. It only became worse as she spent a solid month of almost around the clock work to try and free Shinji from Unit-01, followed by the result of that event and the hard impact Yui Ikari's return had upon her. More long hours spent prepping for today...she couldn't even remember when the last time was that she had slept for more than a couple of hours at a time, or when she had last eaten a decent meal. She was doing well to even remember her own name these days.

Tired, exhausted, neither of those words could describe how she felt right now, she was so far beyond the meaning of either of them. And not just in regards to her overt condition. This went deep into her bones and into her soul...if she even had one left after everything she had been a part of. The last few days had only served to drive that point home like a sledgehammer. She was too exhausted and feeling too broken to even break down. The one saving grace of that was at least she would save herself the embarrassment of going to pieces in front of the entire bridge staff. Speaking of whom, they were all looking at her, unasked questions in their eyes about what Dr. Ikari had said about Kyoko Soryu, about what they should do.

"Dr. Akagi," the gentle voice of Sub Commander Fuyutsuki broke into her thoughts as his hand gently gripped her shoulder. He steered her to a nearby chair.

"I'm...sorry sir," she shakily apologized. "That was an unforgivable error for me to make."

"We've all been there doctor," he assured her quietly. "We've all pushed ourselves beyond our limits in these endeavours, yourself more than most. Remember though, there are those who would help us carry the load if we would let them."

She didn't miss his meaning as she followed his gaze to Maya Ibuki's station. The little tech kept shooting worried glances at her as she went about her duties. She offered the girl a slight, tired smile to let her know she was okay. Maya always wanted to help, to do even more than she already did to help take the load off of her but she rarely allowed her to. She had been involved in too many dark secrets and wanted to keep the innocent girl as far away from that as she could.

She hadn't placed enough trust in her or the other staff to delegate more responsibilities to them, continuing to do things herself that they could have done just as well and eased some of the burden she carried. Maybe now with the way events had gone she could start do that. If she had done it this time around she wouldn't have been in such a state that she would come so close to making such a grievous and potentially deadly error.

Nothing like nearly costing someone their life to sober one's thoughts and sharpen their hindsight. Still, she got the point, both the professional and private side of it, and offered a slight smile to the older man. She knew what he was trying to do. All along Maya had been offering her a shoulder to lean on as well as one to cry on and Fuyutsuki was urging her to take the friendship and support that was being offered. Especially now that she was free of Gendo and all the negatives that relationship had brought to her life. She just might take the young woman up on it. Evidently the old man was even more shrewd than she thought.

She looked to Yui, who had returned her attention back to the readouts before her. She knew she would need to talk to her about a number of things and this incident was now on that list. She just hoped the woman would forgive her for what she had nearly done.

"Sync rate has stopped rising and is now slowly dropping," Maya announced.

"The brain waves are slowing and are starting to drop into a synchronous pattern," Hyuga announced. "But there are still three patterns, I don't understand this."

"It's because there are three minds at work within the Eva," Yui calmly told them. "When I was inside the Eva you only ever saw two patterns, correct?"

"Yes ma'am," he responded. "That of the Eva and of the pilot."

"The Eva's pattern was a combination of mine and the resident consciousness of the Eva itself," she explained, getting a shocked look. "My soul within the Eva was to act as a buffer between the raw animal consciousness of the Eva itself and the pilot, otherwise the pilot's mind would have been overwhelmed by the beast. But in order for the Eva to function properly, I also had to be in sync with the Eva itself, essentially becoming one with it during the periods of pilot synchronization. It also allowed me to control it when Shinji was incapacitated."

Most of the bridge staff turned pale. Hyuga gulped and forged on. "So...when Unit-01 went berserk..."

She smirked. "That was me going Mama Bear and protecting my son."

"...Scary," was the whispered reply from somewhere on the bridge.

"Major Katsuragi hasn't fully been able to sync yet with the Eva individually, so the Eva itself is compensating, " she continued. "It's creating a stable three way sync."

"S-sync rate now stopped and holding steady at 225," Maya stuttered.

"Brain waves are steady and still individual, just short of merger," Yui observed. She smiled. "That means that all three entities are alive and well. He did it. Shinji has synced with the Eva and Major Katsuragi. "

A chorus of relieved sighs went up around the bridge. And a question.

"Umm...Dr. Ikari...why did the sync rate go so high though?" Maya asked.

A tired chuckle came from Ritsuko. "Unless I miss my guess that would be Misato's doing."

"Indeed," Yui confirmed with some mirth. "Having another mind come into contact with yours can be rather startling."

"And considering her fondness for Shinji, she probably went overboard in her reaction," Ritsuko finished.

* * *

 _ **Inside Unit-01**_

 _"That would be a most accurate assumption,"_ an amusedLilith confirmed to Yui through their link.

She supposed she should be angry. After all, she had spent a considerable amount of time preparing Misato for this. She had explained how it worked and what it would feel like, cautioned her about not letting her focus slip until the feeling of synchronization began to feel comfortable and natural to her. Losing focus could mean sluggish responses from the Eva during a fight, or it could mean letting one's mind wander and being pulled too deeply into the pilot's memories and thoughts or letting him be drawn too deeply into hers.

For a newbie to the process like Misato that could be a problem. She was not used to the feel of being in contact with another person's mind. The alien nature of such a thing could overwhelm her easily if she wasn't careful. Getting caught up in another mind's memories, feelings and emotions could in essence drown her own mind in the flow of stimuli.

She and Misato had synced together a number of times already in preparation for today. She could put up barriers to keep Misato from being overwhelmed by her truly alien and more highly evolved mind. The first couple of attempts were rough. She had allowed Misato just enough unrestricted access to her psyche to get the point across. It had spooked her badly and left her a wreck for a couple of hours, but she was nothing if not determined and she began to get the hang of it quickly. Best laid plans however had gone out the window the moment the Eva activated and Shinji began to sync with them. Misato had recoiled at first due to the foreign feel of Shinji's mind but quite soon afterwards she opened up to it and like was often the case with her, she let her emotions lead the way.

The emotional surge had actually surprised Lilith and she had to gather her wits very quickly to keep the level of synchronization under control. She was surprised at how high it had gone before she was able to reign it back. High enough that it had allowed their souls to physically interact within the sea of ever shifting colours that was the metaphysical transition space between the plug and the core.

She realized that she may have also underestimated the depth of Katsuragi's feelings for their Knight of the Throne of Souls. Unless you were able to block or mute them, emotions were easily felt and read during synchronization. Shinji, nor any of the pilots had any skill at such a thing, that's why it was so easy for her, Yui, and now Misato to be able to see and feel his memories and emotions. That worked both ways. She and Yui had been able to block their memories and emotions from him, with the exception of the few instances of minor contact.

Misato however was broadcasting hers like an open radio frequency. In a way, the flood of her emotional output was somewhat like being hit with a wall of sound, the various emotions all being different sounds that all came blaring at you at once. But there was one sound, one emotion that was dominant among the cacophony.

Love.

When she had been testing Misato upon her initial entry into the core she had felt the love that she had for Shinji. That paled in comparison to what she felt being broadcast here, synchronized and unfiltered. There were those that would be appalled by the level of feeling Misato had for this boy that was half her age. But was it really all that surprising? In many ways Misato was really no older than Shinji. That part of her life got suspended in time after she witnessed Second Impact up close and personal. There was already a lot she had missed due to the situation of her parents relationship, but she lost two years of that part of her life while she was locked up within her own mind and living in an institution.

When she came out of it she had to catch up on her education and then was off to college, suffered through her largely one sided relationship with Kaji and then was off to the military, all with her mind tuned towards gaining vengeance on the Angels for what she had suffered. She was immature. She was still that scared and scarred teenage girl from years ago only now she was in an adults body. A body that every man that saw her wanted to play with but held no regard for the wounded soul inside.

But Shinji was different than all of the other males of the species that Misato had encountered. He didn't look at her with desire and lust, or with the hormone fuelled gaze of even his friends. He saw how she acted and how she lived. He saw sides of her that no one else did. He respected her and despite his dismay at some of the things she did, he was actually genuinely happy to be able to look after her, even if that equation was running backwards and she should have been taking care of him. She didn't always say so but she appreciated the fact that he kept the apartment in order and took care of the laundry and cooked for her. He worried for her and about her and it was always a welcome sight for her to come home and see him there waiting for her.

Lilith had seen the depth of hurt inside of Misato. The loneliness and self loathing, the self recriminations toward her feelings for the gentle boy she had to keep sending out to look death in the eye. She hated herself for how she felt and it was added to the pile of reasons for her to justify being drunk almost as much as she was sober. Even that led to more self hate as she knew that too many times Shinji had been the one who had to clean her up, put her to bed, and clean up after her.

Lilith smirked. No, she really couldn't be mad that Misato had let things get out of her control when they synced. It had almost been inevitable really and what she was seeing before her now was worth the price and brought a smile to her face.

The current sync rate wasn't enough to send Shinji into the core, but into a space in between...a transition space that was something like a halfway point where the souls of the pilot and the souls within the Eva could interact. It was more or less an empty space of swirling colour similar to the effect the pilots saw when the Eva was undergoing startup.

The default setting of the soul world inside the Eva, including the transition space, was nudity, a baring of the body as well as the soul and leaving nothing hidden. Right now a very naked Misato had her arms and legs wrapped around an equally naked and full body blushing Shinji, his head buried about as deeply as it could be between her large breasts. As expected he seemed to be frozen in a state of indecision. Did he go with it or try to get away? But when her excited and happy babbling about seeing him again and the sync working stopped, and the joyful tears she was shedding turned to an all out purge of everything she had kept bottled up for so long, his arms went around her and he held her tight.

She let them be for a few moments before moving to join them. She needed to calm them both and slowly reduce the level of synchronization and she also wanted a little 'naked hugging on Shinji' time herself. She had gained a great deal of affection of her own for the boy and this was an opportunity she didn't want to waste.

She also just happened to like the bodily contact in general. She had been held a number of times by Yui as she struggled to regain some semblance of herself, and she had held her previous partner on occasion when her self regrets and sorrow over what had been done to her son became too great for her to contain. She had also held Misato as she broke down when the enormity of it all hit her and played upon her own fears and regrets.

Shinji would soon find himself buried in the flesh of another impressive set of breasts, dark tan in hue this time, with an enthusiasm that seemed to surprise even the owner of said assets. Eventually she simply introduced herself as Shogoki, as he had guessed she was indeed the soul of the Eva itself, also telling him that his mother could elaborate further upon who and what she was for him. For the next half hour she coached them on syncing together as she gradually and safely lowered their combined rate down to Shinji's normal level of synchronization.

Then someone, specifically a certain bearded, white gloved, orange glasses wearing bastard that they all deeply despised, decided that syncing wasn't enough and they needed to run the Eva through some low level movement and weapons drills to make sure it was really working.

Too bad they couldn't have used him for target practice.

* * *

Please leave a review if you would be so kind.

And while you're here, check out my other stories.


	10. Chapter 10

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

 **Transposed**

 _ **Chapter 10**_

 _ **Tokyo 2. International Hotel and Mall Parking Garage:**_

Kaji was on his third nervous cigarette when he heard the squealing of tires as a car was making its way up the concrete ramps of the parking garage. He doubted that it was his contact, he couldn't see them making that much noise or even being last to the party. He suspected that they had arrived here before he had and had been watching him from the shadows until they chose to make their entrance. Chances were pretty good then that whoever was coming up the ramp was with his pursuers, unless he got really lucky and it was just someone looking for a parking space. He seriously doubted that he had that kind of luck though.

He almost rolled his eyes when he saw the car come into view on his level of the garage. Typical dark, nondescript four door sedan and he already knew that the goons inside it favoured dark suits. Someone at SEELE had watched too many old movies and had taken their cues straight out of Hollywood central casting. The whole thing just screamed 'look at us, we belong to a dark, shadowy organization involved in countless dark conspiracies, but don't say anything because it's a secret'.

 _"Could they be anymore clichéd ?"_ he thought. If the situation wasn't so serious he would have laughed.

The car pulled to stop with him pinned in its headlights. There was no point in him trying to hide from them here, they had numbers and weapons on their side, so he stayed where he was with his back to one of the big support pillars. Four men got out of the car, each standing behind the cover of the doors and he heard more people coming through the stairwell door that he had entered from earlier. This was certainly looking like it was about to become a real cluster fuck for him and it only got worse when he saw the telltale red dot of a laser sight moving around on his chest. If he squinted he could see someone at the window of an building across the street aiming at him. He supposed that was what he got for showing up too early and giving them time to set up on him. It was an amateurish mistake.

He was about to engage in a little gallows humour and say something witty to his pursuers when he and they heard what sounded like a muffled rifle shot. At first he thought the sniper had fired but when he didn't feel a bullet tear into his chest he noticed that the window across the street was now empty. That and half of the black suited goons were looking up. He had half a second to realize that the shot had come from the garage one floor up before things went to hell around him.

To his left he heard the familiar sound of a sound suppressed weapon firing. The softened sound of its discharge and the clacking of the bolt told him it was not a pistol but a sub-machine gun. A split second later he heard another open up close on his right just as a large hand grabbed his shoulder and roughly threw him to the floor.

"Stay down there and don't move," a deep male voice commanded. The tone of voice made it clear that he should do exactly that and nothing else until told otherwise. He glanced up to see a large man dressed in dark clothing standing between him and the SEELE guns, spraying them and the car with bursts of suppressed gunfire from another SMG.

The headlights shattered on the car dropping the garage back into its usual dimly lit gloom. He could hear the tinny smack of rounds hitting the car's bodywork, the shattering of glass, the exploding of tires and the softer, wetter slap of rounds hitting flesh and men grunting and screaming in response. A few rounds smacked into the concrete pillar a few inches above his head and he made himself as small as possible, getting rather intimate with the concrete floor. It sounded like the goons were using suppressed weapons as well.

The big man moved away from him, circling to the right to flank the car, snapping off short bursts to keep the heads down of anyone who was still alive over there. Off to his left he heard the frantic sounds of someone trying to get the stairwell door open as they swore in a panicked voice at their attacker. The swearing soon became pleas to be spared. A burst of suppressed gunfire was their answer and then it was quiet. As the scent of gun smoke began to burn his nose he heard single shots going off to both sides. Evidently they were taking no prisoners and making sure that no one was playing possum.

"Clear over here," he heard the man speak softly as he walked back to him. He could see an earpiece in the man's right ear with a slim microphone arm stretching across his cheek.

"Clear on my side," he heard a fainter, possibly female voice from farther off to his left. He heard her start speaking again but it seemed to be directed to someone else.

The man stopped in front of him, the SMG he had been firing earlier was now slung over his shoulder and a suppressed pistol was in his right hand. He didn't fail to notice that it was pointed more or less at him even if it was held low.

"You can get up now," he said.

Kaji did so, brushing at his clothes as he did. "I was beginning to think no one was going to show."

He got a good look at the man now. He was tall, six foot eight maybe, and built wide at the shoulders and thick through the chest, looking strong as an ox. He was Caucasian with an inflection in his voice that he couldn't identify. His black hair was neatly cut and his green eyes bored into him as if he was trying to examine and judge his soul. It was more than a little disconcerting.

"The meet was for ten and you were early," the guy said evenly. "You were on your own until it was time."

"Harsh," he quipped. "They could have taken me and the information I have."

The man smirked. "They weren't leaving here alive in either case. And we already have the information."

"What?" Kaji nearly choked on the word.

"Their friends back in Tokyo 3 paid a visit to the contact you left a copy with and tried to kill them for it," the man explained easily. "Some friends of ours took care of it."

"Son of a..." he breathed as he fished out a cigarette and lit it. "I was sure I made that drop without being seen."

"You're not a very good spy are you Mr. Kaji," the woman's voice said from his right as she stepped into view. "No better than you are with the ladies it seems."

The last time he heard a voice with that particular accent, it was at an arms trade show in Germany and attached to an arms dealer from the United States, Texas if he remembered correctly. He was about to make a witty remark to defend his lady killer reputation when his eyes landed on her. Damn it...the woman belonged on the cover of a magazine. She was dressed in black like her male counterpart and was tall, six feet if he had to guess. She was gorgeous, with long black hair tied out of the way in a long braid and a pair of vivid blue eyes that cut right through him like a knife. Evidently she was as hard and serious as the man seemed to be.

"I've lived this long so I can't be too bad at it," he quipped instead, choosing to defend his competence at his chosen profession.

"We've had eyes on you since before you left Germany, she said. "And you've never known the difference."

"Why would you have been watching me?" he asked, now seriously concerned.

"Because one of the masters you serve is SEELE." The name of the organization rolled off her tongue with obvious hatred attached to it. "That's enough reason but you are also the guardian of one of the pilots and merited watching."

"Even if you are trying to serve three masters, the fact that SEELE is one of them makes you of interest to us," the man said.

Kaji let out a long sigh. "Ikari and SEELE have me spying on each other for them and the JSDF is mostly concerned with NERV. You could say they are my real employers."

"I thought your crusade was a personal one," she countered, staring him down.

He was almost too shocked to respond to that. "Just how much do you know about me?"

"More than I ever wanted to. Pig." she muttered in disgust. He had the distinct feeling she'd like to cut his balls off and feed them to him.

"So why did you contact us instead of giving this information to your employers at the JSDF?" the man asked.

"Because I'm pretty sure SEELE has their fingers stuck in that pie too," he answered. "The chances were far too good that they would be able to suppress it before it could get to anyone who would be able to act on it."

The woman turned her head, listening to someone in her earpiece. "Roger that," she acknowledged. "We'll be waiting for you." She turned to her companion. "The rest of the SEELE agents out on the street have been neutralized and the entire block is clear. Our ride is on the way up. Clean sweep and we're untouched."

"Good news all around then," he nodded with a slight smile.

"So," Kaji began. "Since you know who I am, any chance I can get names here, even if they aren't your real ones? A little awkward to be pointing or calling 'hey you'."

The man's hard gaze shifted back to him and the pistol he held was now aimed at his chest. "Now what would be the point in that?" he asked. "You do remember don't you that we really don't need you, we already have the information you wanted to give to us."

' _This is so not good,'_ he thought. Apparently the sparse whispers he had heard about the SIS being hard were not just idle gossip. "Let's not be too hasty," he said. "There may be things that Ikari told me when he gave me the information that might be useful."

"Hmm, let me think about it," the guy said. Two seconds later he cocked the hammer on his gun.

"Wait!" Kaji exclaimed, holding his hands up in front of him. He heard the sound of a suppressed firearm going off from his left and something struck him in the neck. He stopped as if someone had hit a pause button before his eyes rolled back and he collapsed in a boneless heap.

"Nice," the woman said appreciatively as she regarded the tranquilizer pistol in her right hand before re-holstering it at the small of her back. "They were right, this stuff works fast. Though, I was hoping to see a more panicked look on his face."

Her partner shook his head in mock sadness. "So cruel," he said as he holstered his pistol and went to work checking the unconscious man's pockets.

"Hey, I could have kicked him in the balls first," she countered. "Fucker deserves it. He's a sleazy pig. I mean, stubble and a ponytail? And that cheap ass cologne? Really?" Her look became a little darker. "And the way he treated Katsuragi makes me sick." She smirked at him. "Besides, I seem to remember that the idea to make him think we we're going to just kill him was yours. You don't think any more of him than I do."

"Heh, guilty as charged," he admitted as he pulled a CD case and a thumb drive from the inner breast pocket of Kaji's jacket and handed it to her. "He has no idea how to treat a lady."

"Oh and you do?" she grinned.

"Haven't heard you complain yet," he said as he effortlessly hauled Kaji's dead weight up and tossed the unconscious man over his shoulder. He could hear their ride coming up the ramps to their floor. "Though to be truthful, I'm not sure you actually qualify as being a lady."

"Well fuck you very much, you frostbitten Canuck," she drawled in an exaggerated fashion as she gave him the finger. "Just for that the beer is on you when we get back to the safe house." Her look turned more serious when she looked at the items he had given her. "Were probably gonna need it. I get the feeling that what we just got our hands on is pure nightmare fuel."

"Roger that," he said.

A few minutes later they were disappearing through the night and back to their base of operations in Tokyo 2.

* * *

 _ **A Bit Earlier, NERV Facility, Tokyo-3:**_

Yui Ikari was feeling many different things as she sat on the bench outside the male pilot's locker room waiting for Shinji to get cleaned up. Mostly, she was angry. _Very_ angry. Damn that bastard Gendo! The activation test should have been enough but once that was done he ordered a series of functionality tests. For three more hours Shinji had to put the Eva though its paces testing movement, mobility and weapon's handling. That was too much time spent in a new synchronization all at once. While she knew full well that they needed to have the Eva operable before the next Angel showed up, it wouldn't do them any good to have the pilot so mentally fatigued that he couldn't pilot at all.

She had also been plenty angry at Dr. Akagi, but at least the woman had an excuse. She was the next thing to the walking dead, her level of exhaustion so high that it was a wonder she hadn't collapsed. She remembered all too well her own experiences with the long hours she had put in while developing the Evangelion and she had made enough errors of her own because of it. Her errors at least wouldn't have resulted in someone having their soul torn apart, but she couldn't really call her out without sounding like a hypocrite. She hadn't been very good at delegating things to others or accepting help in getting things done either.

She was also feeling the crushing weight of guilt again of what she had helped push her son into. It had been hard enough to see him get into the plug but when things had started to go out of control she had nearly panicked. She didn't know how she had managed to remain as calm as she did on the outside, while on the inside it felt like she was being eaten alive. Regardless of what Gendo had done she had indeed sent her own son down this path. She had placed him in harms way and now she had to somehow live with the guilt and keep her composure every time she had to watch him get in the plug. It would only get worse when he had to go out and fight the next Angel without her being with him.

She was also a bit worried about something else. The fact that now it was known that the resident consciousness of the Eva was far more evolved than anyone knew. She and Lilith had acknowledged the possibility that things could go haywire during synchronization, there simply hadn't been enough time to truly prepare Misato for what it would be like. They also hadn't given enough thought to the fact that Misato was a person of raw emotions that were never far from bursting forth and the effects that might have.

If the gaps between the wave patterns for Misato and the Eva had been closer together she could have given everyone an explanation that would have been believable, passing it off as a shadow reading or as an expected occurrence. But with them being as far apart, as distinct, and as strong as they were, she had little option but to tell the truth. Or at least as close to the truth as she could get at the moment.

It was inevitable that SEELE would find out and she could only hope that Kiel was unable to figure out what it meant or that he would chose to see it as no impediment to his plans. He may or may not ask Gendo about it when he contacted him for his official report on the test, but it really didn't matter anyway. So long as the Eva worked that was all Kiel was likely to care about. As long as it continued to function, kill the remaining Angels and be there for his plan to take place, there would be little point in complaining about anything else. The game was too far along now for this to truly present an issue.

She hoped.

 _"I'm sorry that things went out of control as they did,"_ her partner apologized. _"I had hoped to be able to contain any potential outbursts but I wasn't able to do so and remain in sync."_

 _"We knew there was a risk of such a thing happening,"_ Yui said. _"And while this was not our ideal outcome, it is also not a disaster. The Eva is functional and that's all that SEELE really cares about. If they make any inquiries about the brain wave pattern I'll handle it as best as I can. That's all that really can be done."_

 _"I suppose so,"_ Lilith relented. _"Leaving them nothing to be curious about would have been better, but you are right. SEELE...Kiel...will not likely care so long as Unit-01 can still serve its purpose."_

 _"How is Misato doing?"_ Yui asked.

Lilith sighed. _"She is disappointed in herself that she could not contain her reaction to seeing Shinji again and seeing that he was well. She fears that she has compromised our plans. I have not yet had a chance to persuade her otherwise. Perhaps after she has exhausted some of her self blame I will be able to talk to her."_

 _"She has been through far too much, just like the Children,"_ Yui lamented. _"Although it was humorous to see Shinji's reaction to her rather enthusiastic greeting. And yours as well. I might add."_

 _"I was simply trying to calm them and maintain control over the situation,"_ Lilith answered unconvincingly.

 _"By making a naked Shinji sandwich?"_ Yui questioned humorously.

 _"...I couldn't let Misato have all the fun."_

Yui chuckled lightly. _"It's alright, I know how you feel about him. Both of you."_ She sighed. _"Sadly, that's the most genuine affection anyone has shown him in ten years."_

 _"Between you, myself, and Misato, I don't believe that will be a problem going forward,"_ Lilith returned with some humour of her own.

 _"He deserves every bit of it he can get,"_ Yui said. The self recrimination was evident in her voice. She was one of those responsible for the lack of affection he had suffered in his life.

 _"He did well today,"_ Lilith continued, aware of her long time partner's angst. _"He didn't panic. He was startled for a moment but he refocused and continued on. I am proud of him."_

 _"So am I,"_ Yui smiled. _"Misato is important to him and he was determined not to fail her."_

 _"Hopefully that determination extends to visiting his fellow pilots,"_ Lilith commented. _"I could feel it from him...he is worried about them, but he is afraid to see them."_

 _"He's still out of sorts about last night,"_ Yui confirmed. _"As for seeing Asuka, he's afraid of what reaction he might get out of her, like always, only it's worse now with what she did and what she now knows of the souls within the Evangelions. I had hoped to be able to take him to see them today but the tests took a lot out of him._ She plucked at her borrowed clothes. _"Guess I'll have to wait until tomorrow to buy a new wardrobe too. He needs the rest worse right now."_

 _"No thanks to that miserable excuse of a man,"_ Lilith spat. _"Speaking of which, has he seen fit yet to grant you your security clearances to the base yet?"_

 _"Professor Fuyutsuki is taking care of it,"_ she answered. _"I need my civilian ID's restored first to satisfy UN and government protocols. Unfortunately even with an official push it is still going to take a couple of days. I was declared as dead for the past ten years after all. It will take some manoeuvring to change that with the public authorities without revealing too much, or having the UN decide they need to send someone here to investigate my situation. It's not like we can tell them where I was. We can use the MAGI to alter any electronic records, but someone has to purge and replace the paper documents."_

" _Hopefully it won't take long,"_ Lilith said. _"The sooner we can get access to Terminal Dogma, the better."_

 _"Yes,"_ Yui agreed. _"The sooner we can take action, the sooner we can begin to bring and end to this madness."_

The sound of the locker room door opening interrupted their conversation. Shinji, dressed in his usual white shirt and black pants, his hair still damp and Misato's cross hanging around his neck, shuffled out into the hall. His lips turned up into a tired smile at the sight of his mother waiting for him.

"You did it Shinji," she praised him as she wrapped her arms around him. She hadn't had the chance to congratulate him when the tests were finally done and before he went off to the showers. "I knew you could and I'm so proud of you."

"It was kind of weird though," he said.

"How so?" she asked, taking a step back again. She figured that she already knew the answer and it was confirmed when his face turned red.

"Well...I actually saw Misato," he explained. "I guess it had something to do with how high the sync rate got."

She nodded. "Yes, the synchronization certainly was high enough that being able to see her would have been possible if she allowed herself to be seen. It's even possible at that level to be able to physically interact."

If his face turned any redder he would burst into flames. "T-there was someone e-else there too," he stuttered.

"Shogoki. She is the soul of the Eva itself, " Yui said, confirming what Shogoki had told him. "She was almost as enthusiastic in greeting you as Misato was."

Shinji's eyes almost bugged out of his head. "Y-y-you know?! How..."

With an amused smile she pressed a finger to his lips to silence him. "I still have a connection to her," she said quietly, tapping the side of her head. "I could see what was happening."

His mouth opened and closed like a fish out of water gasping for breath.

"There is something else I am proud of too," she continued. "When Misato began to break down you did the right thing. You held her and let her know that she wasn't alone and that you cared about her. That was exactly what she needed." She reached out and lovingly stroked his hair. "I've seen your life when we were synced and I know how hard it was for you to do that Shinji, but when she needed you, you held on."

"I didn't know what else to do," he said sheepishly. "I-I could feel it. She felt scared and alone. I know that feeling. I felt like I had to do something." What went unspoken was how he had wished that there had been someone to hold onto him when he felt that same way, as he had so many times over the years.

Yui wrapped her arms around her son, making sure he couldn't see the guilt on her face as she held him tightly to her. "I'm so sorry that no one was there for you Shinji. So sorry that I wasn't there where I should have been. I know I can never do enough to make up for that." She had not only seen his memories while synchronized with him, she had also felt all of the emotions that went with them. She couldn't stop the tears that streamed from her eyes at the pain and loneliness he had endured, that she had to take so much responsibility for.

"But you're here now Mom," he said, his own voice tinged with tears as he returned her embrace. "That's all that matters to me."

His ability to forgive her seemed to be as deep as his inability to forgive his father, and she was sure that she was far from deserving of it. But, she would do everything that she possibly could to try and make amends for leaving him alone. If she could help it he would never feel lonely and afraid again. He would be surrounded by people that cared and who would love and protect him just as much as she would. He deserved no less.

"Now there is a sight that does my old heart good," the voice of Sub Commander Fuyutsuki intoned.

"Professor," she greeted as she turned to him, her left arm still wrapped around her son as she wiped away the tears with her right hand.

"Sub Commander," Shinji said as he wiped away the moisture from his own eyes.

"Excellent work today Shinji," the older man smiled. "Well done indeed."

"Thank you sir."

"What brings you down here Professor?" she asked.

"Ahh...," he hesitated. "It's about your...discussion with Gendo about your living arrangements."

A dark cloud seemed to form above her. "Oh? Has he sent you to try and change my mind about staying in the Geo-front instead of out in the city with Shinji?"

Oh that had not been a pretty argument, especially on top of the one about Gendo adding on all of the extra tests for the Eva's functionality. It had been over an hour since then and his ears were still ringing.

"No no, you will be staying with Shinji just as you wish," he assured her. "It's just that there is a slight issue that I am addressing on you're behalf."

"What issue?" she asked, puzzled.

"It may be better if I just show you."

* * *

 **AN:** The OC's that met Kaji are characters that I have been wanting to use somewhere for a long time. I actually had an Eva fic started where they and the Eva crew would foil a SEELE sub plot that takes place after 3I was averted. Problem was that the OC's were going to be way too prominent in the story and that is one of the current banes of fan fiction writing.

OC's are okay in support roles, even significant support roles, but they should never be more prominent than that. These OC's will have a significant role later in this story but they won't be taking it over.

Please leave a review if you would be so kind.

And while you're here, check out my other stories.


	11. Chapter 11

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

This chapter is going up a little early. I'm on vacation this week and won't be around for the day tomorrow so up it goes now.

 **Transposed**

 _ **Chapter 11**_

 _ **At the Estate of Lorenz Kiel**_

The estate was a stereotype. Everything about it, the large manor house at the end of the winding, tree lined lane way. The rolling fields and thick forests that surrounded it. The rich, dark polished wood decor that spoke of tradition and old money. Even the large office done up in dark stained oak, massive bookcases filled with volume after volume of classic literature and texts of the history of the world, every one of them having been read at least once. The aged leather chairs and the massive wooden desk with the antique brass and green glass bankers lamp.

All of it fit what people expected to see of a rich European businessman, a man who had invested early and wisely in numerous profitable ventures and who exercised a certain amount of influence in the upper reaches of society. A man who had worked a lifetime to amass a sizable personal fortune to go with his power and who had retired to his handsome estate to enjoy the fruits of a lifetime of labour.

That was exactly the image that Lorenz Kiel had crafted for the world to see. How better to hide the truth about himself and his aims and goals from the world at large than to layer them under a thick blanket of normalcy. Hide in plain sight by showing people what they expect to see. But that didn't mean that he was not a careful man. Everything he did, every move he made was carefully planned out and executed. Nothing was left to chance. There was too much at stake to be complacent about anything.

But right now the foundations of what he had spent so long building and advancing behind that facade were shaking. One of his most crucial allies had been taken out. He had no illusions that the accident that killed Harold Connelly III was anything but deliberate, he could feel it in his ancient, creaking bones. Predictably, the other members of the organization had begun to panic, but unlike all of the other times something had come along to make them anxious he wasn't able to reason with them or force them back into a calmer state with just the sheer force of his personality.

Connelly was one of the senior members of SEELE and the Instrumentality Committee and his demise at what they all suspected was less than accidental means had hit several of the other members hard. Connelly had been the one that made the wheels turn in SEELE's favour at the UN. When they needed extra funding or to get a watchdog off their back, Connelly was the one to smooth the ruffled feathers, broker the deals and twist the arms to bring things in line.

Without his presence within the UN the opposition they had been fending off might begin to gain a foothold, and the worst of that opposition was the shadowy Special Investigation Service. Thus far they had managed to keep them at arms length and out of any of anything serious. Without the knife that was Connelly at their throats there may well be a few people that would feel the need to clear their consciences of the things they had done to aid SEELE along the way. Nothing that should lead them even close towards the Instrumentality Committee, but enough to instigate some investigations and turn over several stones.

Fortunately they were close enough to the end game that anything that might come from that should have little or no effect. Even so, Connelly's demise had spooked several of his fellow conspirators and at least a couple of them were planning on going to ground and laying low. Fools. If they weren't under suspicion before their actions now would only draw attention that they didn't need. As tempted as he was to have them eliminated that would only sow more panic among the others and bring the whole Committee down. Still, he supposed he could send people out to have a direct face to face with the wayward cowards and push them back into line. They may be close to their goal, and in the end he would truly be glad to be rid of the fools, all of them, but the scenario wasn't complete yet and they needed all hands on deck to make sure things continued to run a smoothly and problem free as possible.

The good news that Unit 01 seemed to be fully functional had helped to a degree, he knew it certainly gave him some relief, but the situation was still delicate. The First Child was still unconscious in a hospital bed while the Second's mind had gone off the rails. Even if it was the infamous Berserker, he didn't know if one unit would be enough to defeat the remaining Angels. If worse came to worst, Ikari would just have to force his little doll awake and into the pilot seat again despite her injuries. He had never had any qualms about doing it before.

He was somewhat concerned by the brainwave readings from the activation test though. It seemed that the resident consciousness of the Eva itself was far more developed that what anyone had considered possible. Had it become aware? Was it capable of intelligent thought? The nature of the unit's resident consciousness was a cloudy subject. Short of direct contact there was no real way to know what it was or how it worked, if it just followed the will of the human soul that was forced together with it or was it capable of adapting itself. Only one person could really shed any light on that subject. Perhaps he would need to speak with Yui Ikari after all. He needed to determine if this posed any danger to the project.

There was still one other recent occurrence that he still didn't know what to do about. Kaji Ryoji and his sudden and hasty flight from Tokyo 3. He still didn't know what was going on there. The people that had been keeping tabs on the spy in both Tokyo 3 and Tokyo 2 had not been heard from or seen in nearly twenty four hours. There was not a trace of them or of the spy himself. It was setting alarm bells off in his head but he had no information to work with. Was it more of the man's triple agent lurking, trying to uncover information he would never find? Had he just decided to run from all parties involved, or had one of his other benefactors gotten tired of him and taken him out and anyone who was seen watching him?

He was at a deficit for intelligence on this issue and he didn't like it. The chances of Kaji finding out anything truly useful were very remote but not impossible. Possible leaks were things he had accounted for in his planning and he had people that specialized in finding them and plugging them. No matter what had transpired with the spy he needed to know and would need to put those people to work. Just as he would have to do a little extra work himself to bring the scurrying chickens of the Committee back into line.

Living for as many centuries as he had on this world, if nothing else, it had reminded him of the value of patience, a deficit of which had made all of this necessary for him. He had planned thoroughly and carefully and everything would fall into place within his hands. Time and the proper application of influence would see him get his way.

* * *

 _ **Tokyo 3: Misato's Apartment**_

To say that there was a slight issue with the apartment was like saying an Evangelion was big. The description was true but not terribly precise. To be accurate the apartment looked like an Eva had rampaged through it. There were numerous holes in the walls and broken windows. Furniture was broken and seat cushions ripped open. Cupboard doors were pulled off their hinges, dishes were smashed and dry food goods were strewn about the kitchen. The fridge door was hanging by one hinge and the remaining food in it and strewn around it was starting to go bad. The bathroom shower head was broken, but luckily the water pressure was low enough that the excess was going down the drain and hadn't completely flooded the bathroom. Clothes and linens from all of the bedrooms were strewn around the apartment, some ripped and torn, others just flung about.

It was a disaster area, all courtesy of Hurricane Asuka and it was a sad testament to what her state of mind had been. Fuyutsuki had sent people ahead to check the apartment before Shinji's tests were over, having known Yui's wishes about her living arrangements. After hearing about the condition of the place he had wasted no time in commandeering the bigger, empty apartment on the building's top floor. The rooms were all a little bigger and there was another bedroom, overall it was a much better living space.

Shinji had looked rather lost as he had stood amid the carnage. That apartment had become his home and he had taken a certain amount of pride in looking after it and keeping the place as neat and tidy as he could in spite of his room mates. It didn't help much either that his S-DAT player was among the wreckage, singled out for extra special destruction if its pulverized condition was any indication. Luckily he didn't get a lot of time to dwell on it as he had been pretty much tackled by a panicked and madly squawking PenPen shortly after discovering it. It took a while to calm the bird down.

Thankfully the new apartment already had a fridge, stove, washer and dryer. None of those appliances in the old apartment were usable now. The crew Fuyutsuki had sent moved PenPen's fridge for them, which was largely undamaged, and helped them move a couple of dressers that were usable. Everything else was trashed and they would have to go out in a day or two and purchase new furniture.

It was one o'clock in the morning as Yui silently slid the door to Shinji's room closed and smiled to herself as she walked back to her room. Despite being tired from the tests he had worked tirelessly as they salvaged what they could from the old apartment. He had even made a quick run to the nearest convenience store to get some food and cleaning supplies. Other than a little dust the new place was pretty clean so it didn't take too long, but he insisted on washing all of the clothes and linens they had been able to salvage.

It had given her a spontaneous opportunity to tease him a little during dinner. While her borrowed hospital scrubs were in the wash she had been going through a pile of Misato's clothes. Except for a noticeable difference in the bust, they were both close to the same size. As she was looking she happened to spot something that triggered a memory she had gained from syncing with Shinji. A memory of his first night in Misato's apartment.

When she came to the kitchen wearing a pair of denim cut offs and a short yellow tank top, she thought Shinji's jaw was going to hit the floor. In part it was due to the sense of deja vu, and in part it was because he never expected to see her wearing something like that. Giggling, she hugged him and explained herself, apologizing for teasing him. He even managed to chuckle about it himself in the end, at least until she started teasing him about running out of the shower and giving Misato the full show.

As she detoured and grabbed a bottle of water from the fridge before continuing to her room, she couldn't help but wonder why she had acted that way. It wasn't really in her nature to tease as much as she had, yet she hadn't been able to help it. It had been harmless fun, and Shinji had even been genuinely laughing through his crimson blushing. She also seemed to get angrier much quicker than she used to.

She couldn't help but wonder if it had anything to do with exposure to the minds and memories of others through the Eva, especially in the transition space between the core and the plug where the most unhindered form of mental contact could take place if it wasn't actively blocked. Or, maybe it had something to do with inevitable changes taking place within herself after being locked away inside the core for ten years. That had taken a toll on her in various ways that could possibly lead to different behaviours. She didn't think anything serious would come of it, or at least she hoped so, but it might not hurt if she kept an accounting of her actions for a while just to make sure. There were bound to be other differences and more incidences of changes within her.

Sliding her door shut, she made her way back to her makeshift workstation. A couple of cushions to sit on as she let her back rest against the wall, and a laptop sitting on a cardboard box that served as a desk. Fuyutsuki had given her the computer before he left along with her new NERV security card. He had put a rush on it and under the circumstances it mattered little right now if she had her new civilian ID yet or not. The public authorities could wait their turn and would just have to accept NERV's explanation that her whereabouts for the last ten years were strictly need to know...and they didn't need to know. They would huff and puff about it but they would relent and process her papers.

Just as she was about to return her attention to the computer screen and what she had been doing earlier, she spied something on the dresser that caused her to turn red. She scrambled to her feet and stuffed the item in a drawer and out of sight.

As they had been salvaging things from the old apartment she had come across a certain...adult toy that no doubt belonged to Misato. She had stuffed it in a pile of clothes she was carrying and had managed to stash it in her room before Shinji put the clothes in the laundry. She knew that he was likely aware that Misato had such a thing, but she didn't need to have him see her with it nor did she think that it needed to be left laying about the old apartment until they packed up all the non-salvageable stuff for the trash.

Of course, by the time Shinji had virtually passed out in his bed after dinner and she went to have her bath, that itch she had been having ever since she came back became front and centre again. And with something a little more substantial on hand to scratch it with than just her own fingers or the pulsations of a hand held shower, she made use of the opportunity. A couple of times. Okay three and she had to clench a towel in her teeth each time to keep from screaming loud enough to wake Shinji up. Chalk up another difference in her behaviour.

Well, it had taken the edge off and she felt a lot more relaxed now. The events of the day and her argument with Gendo had stressed her out. She was beginning to wonder if sexual release was becoming her standard way to deal with stress. It had surprised the hell out of her quite frankly when she and Lilith had fallen into _that_ so readily. They had already connected on every other level during their time in their prison, it had been almost inevitable that the loneliness and despair they often felt would lead them to find comfort and pleasure with each other. She didn't regret it in the least either.

 _"Nor do I_ ," her counterpart's voice echoed in her head. " _And your little prank with Shinji was amusing."_

 _"It did get him to open up a little about what he was feeling when he first came here,"_ Yui added. _"It's a start, and I hope he gets more comfortable with telling me things. After all this time it will take him a while to get used to having me around."_

 _"Just so long as he doesn't hear you having screaming orgasms in the bath,"_ Lilith teased.

 _"Shush you,"_ Yui admonished laughingly as she sat back down at her makeshift desk.

The clearances Fuyutsuki had given her allowed her unlimited access to the MAGI's files, just like her old professor, Gendo, and Dr. Akagi had. She had essentially been reinstated to her old job. She had started with sifting through technical reports on the Eva's and finding herself impressed with the work that Dr. Akagi and her staff had done to both maintain and upgrade them.

She then immersed herself in the files for the dummy plug system. Just the memories alone of that incident both made her blood boil and made her feel sick. Activation of the system had caused a disruption in their ability to control the Eva and both she and Lilith had to sit by helplessly and watch as Gendo's will was done, the Fourth Child crippled while Shinji was forced to go along for the ride to bear witness and have yet more damage done to his already fragile soul and psyche.

And then he locked her little boy away in a dark, solitary confinement cell because he dared to try and defy him and threaten him for what he had made him do. If she could have regained control over the Eva at that point she would have made sure that Gendo had been introduced to the underside of Shogoki's foot.

 _'We will need to do something about the spares,'_ she commented. _"Both to disable the dummy plug project and for Rei's own good."_ Fuyutsuki had told her that one of the levers Gendo always used against the girl was the threat of replacement. With Gendo's intent still unknown, it wouldn't hurt to take away one of his potential methods of control should he see fit to ever try using it again.

 _"Those bodies contain the barest traces of my soul,"_ Lilith said. _"Not enough to give them a soul of their own, they remain blank slates, but enough for me to sense them easily enough."_

 _"Is there any chance that they could be gaining any level of awareness?"_ Yui questioned.

 _"None,"_ Lilithconfirmed. _"I can tell from that bare trace in each of them that there is no self awareness whatsoever."_ Her voice took on an edge. _"They are nothing but what he designed them to be. Soulless, mindless blanks."_

Yui sighed. _"It should be easy enough to take care of at any point. Tougher will be getting into Terminal Dogma for a long enough period of time to extract what we need from your seed body without being seen or interrupted."_

 _"Can Fuyutsuki not run interference?"_ Lilith asked. _"He wouldn't even need to know what you were doing, he would accept even an acknowledged excuse from you and wouldn't question it."_

 _"Maybe so,"_ Yui agreed. _"But Gendo keeps a close eye on him and keeps him busy dealing with other matters he'd rather not bore himself with...like dealing with the city council and civilian authorities. Another layer of insulation between us and him would serve our needs better."_

 _"You're still contemplating bringing Dr. Akagi into this._ " It was more statement than question.

 _"We might not have a choice,"_ Yui intoned sourly. _"I don't really want to bring anyone else into it but Fuyutsuki can only do so much without Gendo being suspicious and interfering. Another set of hands and eyes would be helpful and she could manipulate the MAGI to help keep Gendo in the dark."_

 _"Can we trust her?"_ Lilith asked the obvious question. _"She has been a full participant in his plans since she took up her Mother's position and up until you returned she was still his lover."_

 _"Girl must have been truly lonely and desperate to hope for any love from Gendo,"_ Yui surmised. " _I would have to talk to her more to get a better feel for where her motivations lie now, but I think she's had her fill of him and his plans and her part in them. She has a defeated, broken look in her eyes. I think she wants a way out but doesn't know where to find it."_

 _"Her help would be useful,"_ Lilith conceded. _"And with her as well as Fuyutsuki on our side that would take away the only allies Gendo really has. Not that it would mean much to him to lose them."_

 _"Maybe not,"_ Yui agreed. _"But it would make it a little more difficult for him to move ahead if he decides to continue this madness."_

 _"We need to relieve him of that abomination he has grafted to his hand,"_ Lilith remarked sourly. _"Without it, his options are severely limited for initiating Third Impact. Without it or my seed body in existence, there would be nothing to call to the Angels. Nothing to wake them and make them come here. They would remain dormant in their cocoons and we could hunt the remainder down and eliminate them with little risk of them awakening."_

Yui sighed. _"I hope that we aren't too late. The timetable in the scrolls isn't exact and we don't know if there is a 'point of no return' stage to an Angel's awakening and growth to maturity. If there is and the Angels still awakens, it could appear anywhere."_

 _"The genetic presence of the Eva's may be enough to still draw them here if that is the case,"_ Lilith surmised. _"But it shouldn't be enough to trigger their awakening otherwise...possibly only in extremely close proximity if it does."_

 _"I hope we're on the right track,"_ Yui said. _"I would really like to stop them so that Shinji doesn't have to fight any more of them, especially now that he may not have much backup to rely on."_

 _"That would be the preferred outcome,"_ Lilith agreed. She cared far too much about Shinji to want to see him continue fighting if he didn't need to, even though she would be there with him as always. _"But there is something you once told me about that you referred to as Murphy's Law I believe."_

 _"Anything that can go wrong, will,"_ Yui groaned. _"Yes, unfortunately Mr. Murphy has a habit of showing up when he isn't wanted. He's a lot like Gendo actually. He's a real prick."_

* * *

 _ **Morning, NERV Medical ICU, Rei Ayanami's Room**_

Outwardly, there were no signs of change or movement. Her bruises were perhaps a little darker and she still slept under the effects of a sedative that spared her from feeling the pain of her badly beaten body. But inside, _deep_ inside, it was a different story. Deep inside Rei Ayanami's mind was a vast and infinite stretch of calm water, dominated by a red hued sky full of stars. Everything was still and quiet. No sound to break the silence, no wind to stir the air and water. Yet, the scene didn't seem stifling or oppressive for its lack of sound or motion.

Rei stood in the placid waters. It wasn't very deep, high enough to conceal the wisps of soft blue hair that outlined her womanhood, but not high enough to reach her hips. She had been here in this construct of her subconscious before, both when she was hurt and when she was feeling things she didn't understand or when the events of her life stained her usually stoic features with a hint of stress. It was peaceful and she would swim for miles or just float for a time, letting the peacefulness fill her and let the gentle water calm her. Peace was eluding her now however. Her injuries never carried over into this place but for some reason they had this time. Cuts and bruises, broken bones. Her entire body ached terribly and she could barely stay on her feet.

Competing with it was the internal pain. The feeling of being lost and abandoned and stripped of the only purpose she had ever known. The feeling of having the one person she could call friend be afraid of the truth of what she really was.

"Well now, aren't you a mess," a clear, strong voice spoke.

She looked up to see before her the dark skinned, dark haired, green eyed resident soul of the Berserker standing before her, equally as naked as she was and literally standing on top of the water.

"Lilith," Rei whispered, her voice rough and raspy and tinged with fear.

The woman sank into the water until she was sitting atop it, letting her legs swish back and forth causing small ripples. "You are such a mess that you can't even retreat into the safety of your own mind now without the pain following, can you?"

"How are you here?" Rei asked.

She smirked. "Silly girl, we are the same flesh and the same soul, how could I not be able to be here? Surely you have not forgotten what you are?"

That only seemed to add to her distress. "I am well aware of what it is that I am." she said quietly.

"What you are is a pathetic little thing who would allow a loud mouthed, egotistical child with a superiority complex to try to beat you to death, rather than find a new purpose when the one you were given is no longer valid." The words seemed to hit Rei like a slap and her already unsteady legs nearly gave out.

Lilith sighed. "But then I suppose considering the way Gendo conditioned you, it shouldn't be surprising that something like this happened. He gave you a single focus and a limited future and when things change he doesn't even speak to you, let alone offer you any direction."

"My role in the Commander's scenario was all that was required of me," Rei rasped. "There was no other purpose for me to exist."

"That scenario is dead and nothing he does will revive it in any form," Lilith said firmly. "We will not allow it to ever come to pass now."

"Then...there is no reason for me to continue to exist..."

She never saw Lilith move, but sure enough she felt the hard, stinging slap to the face that had her seeing stars as she fell and ended up underwater. She came back up sputtering and coughing, the hacking causing her already sore body to flare with pain. She couldn't get back to her feet.

"You would rather just give up and die because you can no longer be used like a disposable tool to fulfill a madman's twisted dreams?" Lilith's voice was sharp and hard and her eyes were virtually glowing. "You would rather stop living than find another purpose for yourself, one of _your_ choosing where you can live any way you wish to?"

"I have nothing...I am nothing," Rei wheezed pitifully. "I would not...be missed."

Again, she never saw Lilith move, but in an instant she went from being on her knees in the water to being hoisted above it by her throat and Lilith's right hand. All of the fury of the infamous Berserker burned in her eyes.

"Nothing!?" she roared. "You are not nothing! You are one of the greatest things that can ever be! You are a life! You are Rei Ayanami. You are not a nameless clone in a tank! You are not Gendo's means to an end! You are you, a precious life that now has her freedom within her grasp! The freedom to shape a new life for yourself in any way you see fit!"

She let the clearly terrified girl down until her feet were once again touching the bottom of the endless sea. She placed her hands on her shoulders to keep her upright and looked into her frightened eyes, her own visage much calmer now that she had made her point.

"Do you think that Shinji believes that you are nothing?" she asked calmly. "Do you think that he would not miss you if you were gone?"

Rei nearly slumped out of her grasp. "Ikari fears me now. He fears what I am."

"He doesn't fear you or what you are child," Lilith assured her. "He is simply overwhelmed by everything he has been told and you already know that he has difficulty communicating with people. Especially so with girls and more so with one he is fond of."

"He...is fond of me?" The tone of her voice was incredulous. No one had ever been fond of her. Even the Commander's attentions never came across as containing any such sentiment. Among everyone else she was either tolerated or despised.

"Yes, he is," Lilith confirmed. "You never rebuffed his attempts at friendship and you never used or abused him. And he has always thought that you were pretty and he likes being around you, he just isn't able to articulate such feelings to anyone for fear that he will be shunned or pushed away. It is all he has known in his life since Yui was pulled into the Eva."

"And what of Yui Ikari?" Rei asked. "I was made to look like her, originally made in part with her DNA." Rei was aware of her genetic disposition. She had seen the reports that showed her human DNA had been assimilated and reconfigured by her Angelic genetics. For all intents and purposes her DNA profile marked her as an Angel, not a human or even a hybrid of the two.

"What of her?" Lilith queried. "She has no quarrel with you. You are a victim like so many others in this accursed place. You have nothing to fear from her. She looks forward to meeting and getting to know you. She also wants to apologize to you."

Rei was puzzled. "Why would she feel the need to apologize to me?"

Lilith sighed. "At the time of her contact experiment Yui was a supporter of the Instrumentality Project. It wasn't until she had a great deal of time in the core to reflect on things that she realized how wrong the idea of Instrumentality was. It was driven home to her even more when she first synced with Shinji and discovered the life he had been subjected to. If not for her support of the project, if not for her subsequent plan of letting the Eva assimilate her and Gendo's selfish, obsessive response to losing her, you would not have been subjected to all of the things you have had to suffer through. She wants to help you if she can."

Rei didn't understand. They had every reason to fear or despise her, to want her disposed of for being the abomination that she was. Yet they did not. If anything it was the opposite, they wanted her to live and to have a life lived by her own direction and desires. But how could she do that? She had been disallowed nearly all of the experiences that others had that led to the ability to live an independent life. She had been conditioned to believe that nearly all experiences, all emotions were meaningless and would only serve to distract her. She wasn't supposed to live beyond her designated usefulness so what was the point in learning how to live and act like a normal human being?

"The point is in living itself," Lilith answered, having heard her thoughts. "To live is to experience as much of what life and the world itself has to offer as you can, both good and bad. Those two things are necessary to define one another. You have already experienced more than your share of the bad, but you now have an opportunity to experience so much more than that. Why not give it a try? Your life can only get better."

"I have known nothing else," Rei lamented. "It is frightening to even consider such change."

"Change represents the unknown, and the unknown can be frightening," Lilith said softly. "But you would not be alone. You will have Yui and Shinji and I will be there as well when this is all over." Rei's eyes widened at that. Lilith smiled. "I plan on living outside of my armoured shell. I have experienced little of this world myself so I will be learning how to live in it as well."

She placed a finger under the blue haired girl's chin, raising her head so she could look into her eyes. "You came here to this place inside your soul to find some peace and to clear your mind. Maybe through that you will find the answer to what you want to do." She began to fade away. "If you wish to speak to me, I will hear you," she said before disappearing completely.

With Lilith's departure Rei allowed herself to simply flop over, splashing under the water only to resurface and float a moment later. She felt so tired, both from the beating her body had taken and the weight of her thoughts. A life lived for her own purposes and at her own direction. Could she really live such a life? In recent times she had actually spent some thought on what it might be like to live differently than she did, but she couldn't really grasp the concept. She had lived such a structured, regimented, and regulated life thus far that it was hard to start considering things she had always been told to ignore because they bore no importance upon her purpose.

Would she even be capable now of living a different way after all this time living as she had? Or was she exactly what the Second always accused her of being, a lifeless doll that couldn't do anything without being ordered to do it? She hated it, hated being called a doll but she could not escape the reality of her life. Little more than a doll was exactly what she was. She had been made in a lab rather than created naturally by an act of love. She had been manufactured and programmed like a commodity and she certainly was not unique. A tank full of clones in Terminal Dogma confirmed that fact.

Everything she had been taught and learned, every facet of her life had been dictated by the Commander. He conditioned her to be an emotionless automaton with little ability or need to make decisions about her day to day life. Obey. Die on cue. That was all that was required of her. Then Shinji came along. The scared, mistreated boy who piloted in her stead despite his terror simply so she would not be hurt anymore than she already was. His kindness and attempts at friendship made something within her change. Over time she found herself comfortable in his presence, even if nary a word passed between them. He never mistreated her or was put off by her seemingly cold manner. He never spoke a harsh word to her even after she had slapped him for having no faith in his father, an action she now greatly regretted. He had made her smile and made her begin to feel something other than the cold, utilitarian sterility of her too often pain filled life.

He cared about her when and where no one else ever did. Lilith also seemed to care and if she was being truthful, then so did Yui Ikari and they all wanted to help her discover a new way to live, to live a life that was truly her own. She let her mind focus on that and the small collection of warm and positive feelings she had experienced around Shinji. Eventually a small smile came to her. She didn't know if she could really live that new life, but she wanted to try. So long as Shinji was a part of that life she might even succeed.

As the phantom wounds that had followed her into this inner world began to disappear, she thought back to what Lilith had told her."I believe that I am fond of you as well Ikari," she whispered. And he was visually appealing to her too, but she was only capable of admitting one revelation at a time right now.

* * *

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	12. Chapter 12

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

 **Transposed**

 _ **Chapter 12**_

In an isolation room on the side of the NERV medical facility furthest away from the command centre, Asuka lay curled up at the head of her bed. Dressed in a set of generic white hospital pyjamas and with both of her hands, wrists, and her right foot heavily bandaged, she stared vacantly at the door across the small room.

She felt broken, just like her own hands and foot and Ayanami's battered body. She tried not to let herself fall asleep because every time she did she relived the horror of what she had done to her fellow pilot. She relived the feeling of the blue haired girl's flesh yielding and bones breaking under the impacts of her fists and feet. She could still hear the thump and crunch, she could still smell the blood and feel it on her skin. But among the worst of the remembered sensations was Rei's complete silence during the ordeal. She hadn't uttered a single sound the whole time. Not a scream or grunt of pain, not a single word asking her to stop. She just took the beating as if she was somehow deserving of it.

When she did end up falling asleep she would wake up screaming and thrashing and the last time she did she had fallen out of bed, worsening the damage to the already fractured bones in her foot. She had beaten her fellow pilot until her own bones were breaking under the savagery of her assault. Many of her fingers and a couple of bones in both hands. Her left wrist. Three toes and a couple of small bones in her right foot. Her whole body ached just from the emotional strain alone and she felt so tired. Not just from the lack of restful sleep, but from a life lived in isolating anger, grossly inflated pride, and egotistical self superiority that once it shattered had let her hidden emotions out and left her weary to the marrow of her bones.

She didn't really know how else to describe it but a part of her was no longer there, it was just simply gone. Not just spent in anger and now dormant, but gone, burned by the raging flames of her outrage. That other part of her, that mean spirited, angry, arrogant side of her lay in broken, charred shards like a dropped china doll within her mindscape and there was a gaping, ragged hole inside of her where it had lived and dominated her young life for far too long.

She didn't know just exactly when it was that she had begun to feel like there were two distinctly different parts of her and that the more docile, more _human_ part of her was an unwilling passenger trapped on the inside with no control and on a ride she didn't want to take. Maybe it had always there but it didn't become known to her until recently. Was it after Shinji had risked his own safety to pull her out of the volcano, or had it begun earlier when they shared synchronization with Unit-2 while fighting the Sixth Angel? Either way it seemed that there was a common denominator that was involved in both incidents and that was the Third Child, Shinji Ikari.

That nasty part of her had discounted him from the very beginning, even before they met on the aircraft carrier she had dismissed him as unimportant and had scoffed at the notion that he had not only piloted and Eva with no training, but that he had actually defeated an Angel while doing so. She didn't believe it and found it insulting considering how long and hard she had trained to be a pilot. There was no way he could have done what Kaji had claimed, not should his sync rate been what it was when he had never set foot inside an entry plug before.

When they did finally meet, she treated him like something unpleasant stuck to the bottom of her shoe. When she moved into his home, complaining all the way about the accommodations and the way he lived, she kicked him out of his own room, treated him like a slave, and never missed an opportunity to belittle, insult, harass, and humiliate him. She was determined to put him in what she saw as his rightful place and make sure that he knew just how inferior he was to her.

The not nasty part of her identified with Shinji. They had both lost their mothers to the Evangelion and while she had externalized everything and became loud and aggressive to push people away, Shinji internalized everything and became quiet and meek in order to hide from everyone. They were both horribly damaged and no one had seen fit to do the right thing for either one of them. After all, they were just merely disposable playing pieces in someones sick game, what did it matter if they were falling apart?

Unlike that nasty part of herself, this part of her liked Shinji. He may have been beaten down and meek, but he was also kind and helpful and just wanted to be friends despite the ill treatment he received from herself and so many others. He had a strength that he didn't know he had. He piloted a nightmare monstrosity that he had never even known existed before despite his fears and his Father's treatment of him, all so an already grievously wounded Rei wouldn't be forced to do it in his stead and suffer even more than she already had.

Despite injuries, anguish, and fear he continued to pilot. He helped her defeat the Sixth. He hadn't hesitated to go into a volcano and pull her out. He kept up the fight no matter what happened to him, no matter how much pain it caused him. He kept trying to please and placate her and she wished so much that she could have cast off that foul side of herself and apologized for the hell she continuously put him through. She wanted to ask his forgiveness and if in that forgiveness he would allow her to prove herself to him and earn his friendship. But she simply didn't have the strength to fight off that side of herself. It was too entrenched and in control and would not listen to reason nor be shunted aside. She could only watch in misery as her other side continued to abuse him and pretty much everyone else around her.

When that other side exploded and started trashing the apartment it was terrifying and she felt like the anger and hatred was going to tear her to pieces and devour her. It was like being caught in an earthquake, a typhoon, and a tsunami all at once, with a little hellfire thrown in for good measure. If anyone had been able to see her face then they would have seen the emotions of both sides on display. The snarling visage and foul epithets coming from her mouth that would make a sailor blush, and the tears of pain and shame streaming from blue eyes that looked defeated and alone and resigned to a horrible fate.

The beating of Ayanami nearly made her give up entirely, ready to let the furious void of her mind swallow her whole and consign her to oblivion so that she wouldn't have to feel _anything_ anymore. But the expenditure of that rage allowed her an ever widening opening through which to try and assert control one last time. With the very last shreds of her resolve she pushed her way to the fore and by the time her other side had finally exhausted both its rage and their body, she was able to take back that control.

It was a tenuous hold at best for as soon as her other half realized it, it tried to fight back. After she was confronted by Shinji in the hospital hallway there was one last burst but she held on. As she faded into unconsciousness and fell into him, she heard that other half scream in outrage and then shatter, becoming nothing but the broken shell of a hollow and empty vessel that now littered her dreams and her nightmares.

She was frightened and at a complete loss as to where her life would go now. Hell, she was at a loss as to who she even truly was at this point. Was she the angry, arrogant Asuka, the milder, more reasonable Asuka? Equal portions of both? Neither? Had her soul split like her mother's, stripping her of entire aspects of her personality? The doctors had no answers for that yet, it was simply too soon for them to know. She had talked to them a little bit but the real sessions had yet to start. She wasn't allowed any visitors just yet and wouldn't be until they were satisfied that she was stable and wouldn't pose a danger to herself or anyone else.

She wasn't sure that anyone would want to come and visit her anyway after what she had done. She didn't deserve it and wasn't sure if she even wanted them to come. She wasn't sure that she could handle it if anyone did. Besides nearly beating Rei to death she had taken both of them out of the fight, leaving the responsibility of defeating the Angels all to Shinji alone. That other part of her would have viciously swore that that was how Shinji really wanted it so that he could have all of the glory and accolades for himself. She knew that to be the furthest thing from the truth and she hated the thought of Shinji having to face any remaining Angels that may come all by himself.

She curled into a tighter ball and hid her face against the pillow. It didn't do her any good to realize that she may not have only doomed him, but the entire human race as well with her actions. She could only hope that it didn't turn out that way. Hope that once again Shinji could save the day for them all and maybe save her in the process.

* * *

 _ **Tokyo-3, NERV, Terminal Dogma**_

Terminal Dogma, its deepest levels in particular, were the most bone chilling and creepiest sections of the entire complex that made up NERV's Tokyo-3 headquarters. Other than the specific contents of a few labs the place certainly hadn't changed much since the last time Yui walked its dank, dingy, silent as a tomb corridors.

This wasn't how she had planned on spending this particular day. The apartment needed re-outfitting and she needed clothes and going shopping for both would have given her some more relaxed quality time to spend with Shinji. As the morning had turned out though, perhaps it wasn't entirely bad that they had to postpone that shopping day to another time. Besides the fact that it was raining heavily and was just generally a dull, gloomy and miserable looking day, she had started it off by making a very large mistake. After a late night on the computer reviewing files, the smell of breakfast cooking had roused her from her sleep. Being rather groggy and not yet capable of focusing, she had walked out of the bedroom and into the kitchen stark naked.

Shinji nearly dropped the pan he was holding when he saw her, which was a good five seconds before her brain kicked in and brought her up to speed. With a yelp she scurried back into the bedroom and when her heart finally stopped threatening to pound its way out of her chest, she hurriedly put on a pair of jeans and a t-shirt borrowed from the salvaged clothing that belonged to Misato. Naked was the form of the human soul unbound by a physical body, at least inside the world of the Evangelion's core, and that was how she had spent the last ten years. Even though she was restricted by her environment, she still was able to feel and experience things in a way that the physical body never could.

Being back in a flesh and blood body felt...heavy, and clothing, even loose clothing felt terribly restrictive to her now. At some point during her file browsing the previous night she had shed what she had been wearing without much of a thought. It had become too uncomfortable and she would have ditched it before bed anyway, she wouldn't have been able to sleep otherwise. The hospital had been a different story, she had been exhausted so there wasn't much time to think about feeling uncomfortable before she crashed out.

She should have taken into account that she wouldn't be able to just change behaviours so quickly after ten years, and should have left herself a reminder where she would see it before leaving the room or she should have allowed herself to wake up fully before following her nose to the kitchen. But she was hungry and breakfast smelled good and her half asleep mind was running on auto pilot. She was so embarrassed that she didn't even want to leave the room again. She was pretty sure that the last thing Shinji ever needed or wanted to see was his Mom in the buff.

It took a combination of things to finally get her to come out. Her rumbling stomach, the smell of the food, and a nervous Shinji telling her that she needed to eat and that the food would get cold if she didn't come out soon. But most of all it was the guilty tone in his voice as he tried to apologize for what he had seen when it most certainly was not his fault that he did.

A bit of a dam broke inside of her at that point. She opened the door and flung her arms around her son, crying and apologizing for not just the nudity, but for everything. In her head she cursed Gendo and those he had left Shinji with for turning him into the meek and scared boy who tried to apologize for every ill in the world as if he was personally responsible for them. She cursed all of those around him since he came to Tokyo-3 for either adding to that burden or standing dumbly by and watching him slowly drown in it.

But most of all she cursed herself, cursed herself to hell and back for being so caught up in her scientific achievements and her work that she couldn't see what a thrice damned fool that she and everyone else involved with the HIP and Project E were being. For leaving her precious son to the wolves while under the illusion that everything she was doing, everything she was building, was to protect him and his future. She thought she was acting as a caring mother who was looking out for her child. For someone so smart, she was really incredibly fucking stupid.

The ultimate blame for everything Shinji had been forced to endure, the life without love and care, the mistreatment and apathy of those around him. His internalization of the pain and the way he hated himself and took all of the blame that everyone seemed so eager to place upon him was all hers, no one else. She was responsible for every single thing that he had been forced to endure for the majority of his young life.

He even tried to apologize for her meltdown and she practically screamed in anguish. She let everything that had just been going through her mind spill from her lips and begged him to place all of the blame, all of the hurt, exactly where it belonged. Right on her shoulders because it shouldn't be anywhere else. None of it was his, none of it was his fault. It was all hers.

In the end they had cried themselves out, ate their very cold breakfast and decided to forgo the shopping until the next day when the weather promised to be better and they would instead spend the day talking through everything that had come of that morning's mess. It was something they would have needed to do at some point anyway, but since their hand had been forced somewhat that time seemed to have arrived.

Or it would have if it weren't once again for the Bastard King of NERV. The phone rang as they were washing the dishes, with Fuyutsuki on the other end bearing the bad news that Gendo had decided that more tests with Unit-01 were needed to verify its operational status. This time around without Shinji having the opportunity to prepare himself for the unknowns of the first test. It was pretty much a scramble drill...get there fast and do a combat ready start up, then standard tests.

It figured that the miserable bastard wouldn't even have the balls to make the call himself.

Once they rushed to NERV and performed the emergency combat start up...in which all went perfectly fine...she excused herself for the remainder of the tests to attend to some other matters dealing with her reinstatement. And, as she loudly made it known, to put some distance between herself and a certain bearded bastard lest she decide to rearrange certain parts of his anatomy in the most painful way possible. Ways that made every male on the command bridge cringe and want to hide under their consoles. It turned out to be the perfect opportunity for her to make her needed trip down to the depths of the base.

She had just exited the lab that contained the huge LCL tank that housed Rei's clones and slumped against the wall, taking in a deep, shaking breath. Just seeing them had been draining. As soon as she had laid eyes on them she felt sorry for them and again condemned herself as she had earlier. They most likely wouldn't have ever been created at all if she hadn't let the Eva take her and ultimately set Gendo's twisted scenario into action.

The clones were alive, but they had no awareness of any kind. They were nothing more than animated flesh and blood with no soul. They reacted to nothing. No stimulus of any variety would make them react, they just floated through their liquid home oblivious to all else around them. Goldfish were more aware and active than they were. They didn't even react when she stripped down and entered the tank herself to join them, floating around them and observing them.

When she approached the first one and touched her, there was no reaction at all and when she absorbed the tiny fragment of Lilith's essence from the clone and it painlessly turned to LCL, none of the others reacted in the slightest. Not even a hint of the most basic and primal survival instinct of fight or flight, they just continued to drift along as she went to each one of them and repeated the process until there were none left. She hugged each one as she did her work. It did nothing for them, but it was the least that she could do for them even if the gesture only had the slightest of benefits to her own ailing conscience.

She ran a hand through her still damp hair. The shower had cleansed her of the LCL but had done nothing to wash away the guilt she was feeling. Soulless and unaware as the clones were, she still felt unsettled about ending their existence. Her emotions were already raw enough today as it was.

 _"It was the best thing that you could have done for them Yui,"_ Lilith assured her gently.

 _"I know,"_ she agreed sadly. _"They never had a chance. No souls and no chance to ever acquire one. Just spare parts for Gendo's scheming."_

 _"Better for them to be ended by your hand than to be used as cores for the dummy plug or held as a threat over Rei's head,"_ Lilith said. _"He now has two less options at hand if he should choose to continue his game."_

Pushing tiredly off the wall Yui slowly made her way back to the elevator. She swiped her security card through the reader and sent the car down to her next destination in the deepest part of the base.

 _"So how is the test going?"_ she asked her long time partner.

 _"Very well,"_ Lilith answered. _"Misato has much better control over her emotions today and there is very little nervousness coming from Shinji. I sense much more in the way of positive resolve from him since he was told everything and understands the situation much better now. He is no longer piloting just so someone else won't have to. He wants to defeat the Angels and keep everyone he cares about safe. You above all now that he has you back."_

 _"I was worried that what happened this morning would affect him since we didn't get to sit down and talk about it,"_ Yui admitted.

 _"His anger at Gendo allowed him to push it aside for now so that he could focus, but I can feel the worry he carries for you in the back of his mind,"_ Lilith informed her. _"I am worried that his anger at that man will set off all of the pain and rage that we know he has kept stored within him for all of his life."_

 _"I had hoped to have some time to start working on that with him but it seems that events do not want to run in our favour right now,"_ Yui lamented. _"And he didn't need my outburst this morning to add to his worries He has too many things heaped upon him now without that."_

 _"Sadly he knows no other way...and you are his mother. He's bound to worry when you are upset. I will do everything I can from my end to help ease his mind and help him remain calm,"_ Lilith promised.

 _"I know you will and I am grateful that you care about him so much,"_ Yui said. _"I guess all we can do is hope that he can keep it contained a little longer until we can find some time to start dealing with it. It's not fair nor is it the best thing for him but it's all we have right now."_

After a few more moments the elevator finally reached the end of the line, the very bottom most level of Terminal Dogma. Across the wide corridor from the elevator were the massive, thick armoured doors that hid one of NERV biggest secrets. After sliding her security card through the reader the doors creaked and groaned loudly as they slowly began to part. Soon there was room enough for her to pass through and into the immense room beyond.

She wasn't pleased at all with what she saw there. The bloated, white, legless humanoid form of Lilith's Seed body indeed was there hanging from its cross and bleeding a steady stream of LCL into the large pool below. But it was the sight of the Lance of Longinus stabbed into its chest that had her seeing red.

With the Lance in place she could not extract the tattered traces of Lilith's soul that still permeated the otherworldly flesh. What remained was on par with what she had extracted from Rei's clones, only on a much larger scale. Which was why she couldn't figure out why they felt the need to impale the body with the Lance. It was essentially inert and couldn't do anything or affect anything. Certainly not on a scale that mattered. It was no threat.

Fuyutsuki had told her that they had retrieved the Lance from Antarctica, but he hadn't said anything about them leaving it down here and stabbing it into Lilith. The Lance was the greatest weapon they had besides the Evangelions themselves to kill the Angels with and here it was in the deepest part of the base and at the farthest point from where it could do them any good, being used to keep a non existent threat imprisoned and impaled upon its cross.

The scream of frustration that roared from her throat was drowned out by the alarms and Lilith telling her that the Fifteenth Angel had arrived.

* * *

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	13. Chapter 13

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

 **Transposed**

 _ **Chapter 13**_

A stabbing pain shot through Yui's head as she neared the doors to the Command Centre, causing her to slump against the wall and press her hands tightly to her temples. The ride up from the bottom of the base had been excruciatingly slow and by the time she had reached the Command level they had already had Shinji take a shot at the Angel with one of the Eva sized positron guns.

It didn't take a genius to figure out that it would take something like the experimental positron gun they had used to take down the Fifth to reach the Fifteenth up in low orbit and have even a remote chance of breaking through its A.T. field, and it was doubtful if it even would at that range. Evidently the Angel had responded to their attempt.

" _What the hell happened?"_ she queried.

" _The Angel..."_ Lilith sounded strained and ragged. _"It has hit us with a beam of light...it's...trying to penetrate our minds. I...don't think I can stop it. Limit it...possibly...but not stop it."_

The connection went dead and Yui knew that Lilith had cut it off before whatever the Angel was doing could spread to her. She also knew that Lilith would most likely have to cut off or severely limit her connection to Shinji so that her mind didn't overwhelm his if she couldn't limit or slow down the Angel's attack.

As the pain in her head faded away and she took a couple of deep breaths to regain her composure. She couldn't help but think again that the perfect weapon that they needed right now was here but out of reach. The only thing that could retrieve the Lance would be an Eva. Asuka probably couldn't even get hers to move right now if she was even capable of doing anything herself and Rei was still unconscious and it was doubtful if they would be able to wake her up.

She entered the chaos of the Command deck and panic nearly overwhelmed her. She could hear her little boy screaming in pain, screaming for the Angel to get out of his head, screaming that he didn't want to remember. Going to the terminal she had co-opted as her own, she brought up the sync graphs and saw that the lines representing Shinji and Misato were fluctuating wildly, while Lilith's was more in control but no longer in a rhythm with the others.

That was both good and bad. Good in that Lilith's otherworldly mental presence would not overwhelm their minds in the chaos, bad in that they were on their own in trying to cope with whatever the Angel was inflicting upon them. Akagi and her technicians were trying everything they could think of to get the Eva to shut down, thinking it would somehow stop or reduce the attack upon Shinji. What they were failing to realize in the heat of the action was that the attack wasn't dependant upon his synchronization with the Eva to reach him. Even if it wasn't affecting both souls within the core, it would still be affecting him anyway and he was obviously in no condition to even try to get the Eva to move and drop back into the base.

Even she had no idea what to do other than destroy the Angel to make it stop and with the only weapon they had at their disposal that was capable of such a thing being out of their reach at the moment, all she could do was level a hateful glare at Gendo for leaving it down in Terminal Dogma to begin with.

 _"You will pay for this Gendo Rokubungi,"_ she growled darkly within her mind. _"You will pay for this and everything else that you have done to him."_

A chiming from her panel brought her eyes back to the sync and brainwave graphs on the screen before her and a new level of panic shot through her. The wave forms for Shinji and Misato, as frantic as they were, were beginning to harmonize. Despair flooded through her at what she knew was about to happen and there was nothing she could do to stop it.

* * *

 _ **Inside Unit-01:**_

Shinji screamed and thrashed as sharp claws of pain seemed to carve and rip through the depths of his mind. He begged and pleaded and screamed for it to stop, screamed that he didn't want to remember as the claws tore open the thin scabs and scar tissue that tried to cover and hide the worst moments of his life. The memories flooded through his mind, tearing past the weak and pathetic attempts he made to block them and hold them back. Mommy going into the big machine and never coming back. Daddy being so cold, leaving him at the train station and turning his back on his cries not to leave him. The uncaring indifference of his new guardians as he grew up lonely and unloved. The crushing return to his father only because the man finally had a use for him.

Through his own screams and this waking nightmare he was dimly aware of the feel of the connection between himself and Misato. He could hear her. Kami, she was crying and screaming, begging and pleading like he was. She didn't want to remember, she didn't want to relive the past again. By instinct they both seemed to reach out to each other, looking for comfort and safety. Looking for someone to hold onto to make the pain and despair go away. To feel anything other than alone and in pain, to feel anything but unloved and unwanted.

The effect was not what they desperately yearned for. Their minds, their memories, their nightmares crashed together and engulfed them both like a tsunami. The loss of a mother. The breakdown of a family by the father's obsession with his work. A child abandoned by the father. A child caught in the middle, trying desperately to be good for her Mother's sake and sanity. Uncaring guardians. Lonely homes. No contact from a father. A father that tried to reconnect by dragging his child into his work in a desolate frozen land.

A thing of primal nightmares. An incomprehensible giant of light rising into the sky as the earth beneath it is ravaged. A god like vision not meant for human eyes let alone the eyes of a child, cast adrift and bleeding from a wound that would leave its mark for life just as the nightmare image of the giant was burned into a fledgling mind.

The silence, loneliness and isolation of miserable solitude with no warmth. The silence, loneliness and isolation of a mind and body scarred, silenced by fear and trauma. For both there was no one. No one to care, no one to love them, no one to hold them. Alone in their pain their misery. Alone in the mind numbing agony of their isolation.

Withdrawal.

Crawling within himself to hide from a world intent on hurting.

Useless.

 _I'm sorry_.

Worthless.

 _I'm sorry_.

Weak.

 _I'm sorry_.

Coward.

 _I'm sorry._

Bursting from the silence, acting out to shame herself in his memory.

Dirty.

 _Like that?_

Drunk.

 _Are you proud?_

Debased.

 _Happy?_

Whore.

 _Look at me now!_

Together, their voices strained, agonized, rising in anger.

"Empty. So empty. So lonely. It hurts so much, hurts so deep. Why is it like this? Why did it have to be this way? Did we do this? No, not us. Not us alone. We were driven. We were pushed. We were forced and brought to this. Who!? Who did this to us!? Who hurt us this way? WHO!?"

Together their voices, broken ragged and quiet, filled with sorrow and pain.

"Father. Father did this. Father broke us. Ruined us. Twisted us and used us. Father hurt us."

"Father!"

"FATHER!"

"RAAAAAAUUUUUGGGGHHHHH!"

* * *

 _ **NERV Control Room**_

But for the hum and drone of consoles and computers the control room was dead silent. All eyes were on the view screen where the mighty Unit 01 sat sagging on its knees looking up at the sky through the beam of light projected by the Angel. The heart wrenching scream filled with so much pain and anguished rage had silenced everyone. But it was the words before that, spoken in a perfect and pain etched harmonization of both Shinji and Misato's voices that had every person in the room, save one, with tears in their eyes.

Gendo sat as stone faced as ever, perched in his command seat in his usual pose while Fuyutsuki stood at the handrail of the upper command deck, head bowed and holding the rail in a death grip. Maya Ibuki sobbed openly while a crying and obviously guilt riddled Ritsuko tried to console her young protégé. Yui sat slumped back in her chair staring at the screen but not really seeing it. Tears streamed down her cheeks.

This pain, this was the legacy she had left for her son when she and her lofty ideals climbed into the Eva that day ten years ago. She left her darling little boy in the care of a monster who would not give him a single moment of joy, who would not even allow him to remain in his presence after she was gone. Evidently Misato had suffered in her life just as much as Shinji had. She knew about the break up of her parents and of her front row seat to Second Impact and how it affected her, but what she knew beyond that was based upon what she saw of the woman through Shinji's memories of her. She could guess at the rest based upon that and if she was right, it certainly then wasn't pretty.

If she hadn't been so foolish about being on board with the Instrumentality Project then maybe she could have spared them so much pain. Young, foolish, and enraptured by the thrill of discovery with her accomplishments and theories being critical to the plan she let herself be swayed by the arguments put forth by SEELE's cabal of rich and mortality fearing old men. There was nearly as much blood on her hands as there was on Gendo's and people like Misato and her Shinji had paid the price, were paying the price for her hubris.

She refocused her watery eyes on the computer screen before her. The wave patterns of Shinji and Misato weren't just in sync, they were perfectly harmonized. Their ego borders were still distinct, but their thoughts and memories were being shared with each other as if they were their own and as they had all heard they even spoke as one being. The pain of one was terrible enough, but now they were sharing each others pain, feeling it under the Angel's interference and living it as their own.

The line denoting the Eva's consciousness had begun to show blips of agitation as well but still remained distant from the other two. Lilith was keeping Misato and Shinji from being too far in sync with her, the number being just above the bare minimum to move the Eva. With her own wave pattern starting to show signs of agitation that was a good thing. If the Angel began to affect Lilith the way it was affecting them, the last thing they would need was to be deeply connected to her and be left open to her vast alien consciousness. It could very well damage their minds and potentially kill them.

She felt so helpless. All of the knowledge she had in her possession could do nothing for them. The only weapon they had that would kill the Angel was out of reach with no one able to go and retrieve it. Lilith still had her shut out and trying to contact her would only be a distraction right now. She had done so much wrong already, was responsible for so much, and now that she had come to realize it, now that she was back and had a chance to do something positive, she could do no more than sit here and listen to her son suffer.

"Sir!" a technician called up to the command deck. "We have a report from the medical centre that the First Child has awakened and left the facility. She was just spotted near the Eva cages!"

Yui didn't wait to hear Gendo's response to the news. She bolted out of the command centre and headed for the cages. She didn't know how Rei had managed to climb out of her slumber, she shouldn't have been able to yet. That was something else she was at least partly responsible for. Between her injuries and what she had done Rei should still be down for a little bit longer before her S2 organ would start to heal her and quicken her recovery. However, she wasn't about to look a gift horse in the mouth. This was the best chance they had. If Rei could get the Lance from Terminal Dogma, there was a chance to save Shinji.

* * *

 _ **NERV Medical ICU, Rei's Ayanami's Room**_

She awakened with a start, the brief jerky motion enough to send waves of pain through her ribs, head, and numerous of her other injuries despite the pain medications that were no doubt entering her bloodstream through one of the IV's hanging by the bed. Why had she awakened so suddenly? Obviously she wasn't well enough yet. She knew her S2 organ had not done its job yet and the thick, heavy feeling she had all over spoke of the medications she was under. Frankly, there was no way she should be awake right now. Slowly her sluggish mind caught up and her eyes went wide. Ikari...he was in danger. He was in pain! She remembered now. For a brief moment her mind had come into contact with Lilith again and she saw the Eva enveloped in a beam of light. She heard Shinji screaming. He was being attacked by an Angel, an Angel far up in the sky and he couldn't fight back.

She knew NERV's arsenal of weapons, they had nothing that could reach an Angel that high up and penetrate its A.T. Field. Nothing, except the Lance. The weapon she herself had stabbed into Lilith's body down in Terminal Dogma on the Commander's orders. Ikari was suffering and needed her help. With the Lance she could help him. She remembered back to their battle against the Fifth and the words she spoke to him.

"I promised to protect you," she rasped. "That has not changed. I will protect you Ikari." She remembered in the aftermath of the battle how he rushed to her, tears in his eyes and afraid that she was hurt or worse. She hadn't known what to do but she took his suggestion and smiled and it somehow felt right. She wanted to be able to smile for him again and see him smile in return.

With hands that were bandaged from fingertips to elbows she fumbled and pulled off the leads for the bedside monitors and pulled out her IV's, ignoring the trickle of blood the flowed from the tiny holes in her flesh. Painfully, she tried to roll and swing her legs over the side of the bed. Every joint, every... _everything_ hurt. The Second Child been thorough in her beating, no part of her body had been spared from the punches, kicks and stomps. With much discomfort she realized that she was not free of the medical apparatus yet...they had inserted a catheter and it proved to be a very unpleasant ordeal to remove it with her heavily bandaged hands. It also didn't help that _that_ was a part of her anatomy that Soryu had taken great delight in kicking a number of times. She spotted a tint of red in the collection bag that hung from the bed frame. Do doubt that several hard kicks to the kidneys had cause her to bleed into her urine as well.

She looked down to the floor and it looked to be a mile away. She knew this was not going to be easy. Her thighs were heavily bruised and her joints had all been stomped on and ached persistently. She had little faith that her legs would even hold her weight when she slid off the bed. She suspected she likely had broken bones in her feet just like she obviously did in her hands.

As was normal when she was injured, unless there was a ruptured organ, the doctors would not perform surgery. Her S2 organ would repair the damage and no one seemed to care how much pain she would be in until then. Thus they didn't see fit to operate to fix even displaced fractures. They would simply line up the breaks as best they could and heavily bandage her to keep everything in place until her S2 did the rest. In this case it was no different it seemed except for the fact that her S2 had yet to do its work.

As expected she rolled off the bed and her legs would not support her. When she landed she hit the floor with a mighty splat, crying out in pain. She coughed up blood, not knowing if it was due to a bruised lung or if one of her broken ribs had shifted and pierced it. The pain didn't allow her to differentiate. She couldn't let it stop her, couldn't let the pain stop her. Ikari needed her, her friend needed her and if she had to she would crawl all the way to her Eva.

She saw a wheeled examination stool by the door. If she could get herself propped up onto that even part way she could roll herself along. She needed to get to the elevator down the hall, from there she could take it down to a point very close to the cages. It was positioned as such to expedite getting an injured pilot from the cages to the medical centre as quickly as possible.

It took her four tries with the stool jammed up against the wall to pull her body onto it enough that she could make use of it. Three tries to get the door open and three near tip overs before she got the stool rolled away from the wall and to the doorway. She was sweating profusely now, and her breathing was laboured from the effort. Her bandage wrapped and concussed head was throbbing. Her right leg and foot seemed to be in a little bit better shape than the left and she used that to slowly propel herself along, whimpering in pain with every push. It seemed to take forever but she finally made it to the elevator. Just as the doors were closing behind her she heard people yelling for her to stop.

When the elevator reached its destination and the doors opened she pushed off to start rolling. The wheels on the stool caught on the edge of the floor where it met the elevator and she pitched forward and to her left off the stool, slamming into the rough, open metal grating of the floor that stretched from the elevator to the Eva's umbilical bridge. She cried out loudly in a prolonged surge of pain. Fighting it down she began to crawl across the rough metal, she didn't have time to try and get back on the stool and it wouldn't roll very well on this surface, especially with her weak ability to push it. The rough metal bit into her as she pulled and wormed her way along, tearing at her hospital gown, her bandaged wounds and her bare flesh.

An eternity later, at least to her mind, she reached the smoother surface of the umbilical bridge. Luckily the path from the elevator to the bridge was closest to her Eva than any of the others but the shorter distance was little consolation to her right now. At least no one was here to stop her. With only one Eva operational and it being out now taking on an Angel there was no need for personnel to be in the immediate area until it returned.

They weren't there to stop her but they weren't there to help her get there any faster either and they wouldn't unless the Commander ordered them to anyway. By the time she got to the ramp leading up to Unit 00, she was a total wreck. Well, more of a total wreck she supposed. The bandages on her hands and arms were torn and bloodied with some of her fingers being crooked and at odd angles because she had dislocated them again or displaced them at the breaks. She had several fresh bloody scrapes up and down her legs and she had left a thin smear of blood across the umbilical bridge.

She was sobbing in both pain and frustration now. She wouldn't be able to crawl up the ramp, she would have to try and use the handrails to move herself along. If she could haul herself to her feet and lean over the railing she might be able to move herself along. She had to, she had to keep moving. She couldn't stop until she made it to the Eva. It didn't matter how much it hurt, it didn't matter how much further damage she did to herself, she had to make it. She had to get to Shinji.

With all of the might and determination she could muster, she reached up and grabbed the end post of the railing. More tears and cries of pain escaped her as she forced her shaking arms to pull her and the seeming dead weight of her legs to move and get under her weight.

"Shinji needs me," she cried. "He needs my help." She repeated it over and over like a mantra even as her body shook mightily from her efforts and her head throbbed and swam, her vision dotted with black blotches. With a final heave she made it, hanging over the angled rail and dry heaving. With her only sustenance having been from an IV there was nothing for her stomach to expel. Continuing to sob out her mantra, she inched along the rail, forcing her weak, shaking legs to follow and hold what little weight the rail wasn't. The pain from the rail pushing into her broken ribs was excruciating.

Inch by agonizing inch she made her way along until she all but collapsed across the control panel outside the waiting entry plug. With her vision beginning to go double on her as well as dimming she managed to enable the automatic entry procedure and start it up. With a final lunge she fell across the distance between the console and the plug.

Hooking her elbows over the edge she put all the energy she could muster into a final pull and tumbled headlong into the plug. A moment later the door closed and the plug began to fill with LCL. Once there was enough for her body to become buoyant, she managed to give enough of a push against the side of the plug to send her drifting to the pilots chair where she let the rising liquid do most of the work to get her into the seat.

She could hardly see now, her vision edging to black and back and her head felt like it was going to explode. She tried to control her breathing to take a proper lungful of the LCL but it was impossible and she choked and gagged on it causing fresh waves of pain to slam throughout her abused body. Luckily the direct oxygenation of the energized LCL kept her from suffocating until she could breath again. She was more than spent physically and she was barely hanging on to consciousness but she couldn't stop yet. If she could just remain awake her thoughts should be enough to control the Eva for what she needed to do.

She began repeating her mantra again as she heard the systems starting up and coming on line. Start up messages scrolled on the wall before her and she heard the sound of the LCL filter pumps coming to life somewhere behind her. The plug began to lighten and colours scrolled along its inner surface. She readied herself for the feel of the Eva connecting to her as the sync began. She felt the barest beginnings of contact when suddenly everything stopped and went dark and silent. In what passed for panic for her she jabbed away at the controls in front of her until she set the restart. The process started again and this time there was more contact but it was not pleasant. It felt mocking and full of malice before the system once again shut down.

"No!" she cried hoarsely, more tears streaming from her eyes and into the LCL as she flailed and fumbled at the controls. The consciousness of the Eva was refusing to cooperate with her. When she needed the difficult, ill behaving thing the most it was refusing her. The brief contact felt like it was actually mocking her.

"No!" she cried out again. "He needs me. Ikari...Shinji needs my help. He will die if I do not help him."

She continued to flail uselessly at the controls, crying and repeating her need to help Shinji. She didn't even notice when the plug shuddered and rotated out. Didn't notice as the LCL drained. Didn't notice as she coughed and choked to spit out the fluid from her lungs. She didn't notice when the door cycled open and Yui Ikari rushed in and wrapped her arms around her.

"No!" she cried weakly. "I have to help him. I have to...I have to...help him...I have to...Ikari-kun...I have to..."

The tattered girl passed out in Yui arms, the woman crying as she held her knowing that her son's best chance had failed.

"Thank you for trying so hard Ayanami-chan. You did everything you could. We have to leave it to Lilith now. I know she will not let Shinji die, no matter what it takes."

She just hoped that whatever that was, it would happen soon.

* * *

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	14. Chapter 14

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

 **Transposed**

 _ **Chapter 14**_

 _ **Unit 01's Core**_

She remained as distant from them as she could for their own safety but it was killing Lilith not to go to them. Through her synchronizations with them she was already well aware of the pains of their lives and their own respective versions of hell that they had lived and continued to live out. But hearing them be in so much pain and reliving that anguish, reliving each others pasts and present as if they were their own, it cut into her deeply. She cared for them both and they had already suffered far too much. They didn't deserve to be subjected to this cruelty.

While the Angel's assault wasn't reaching into her mind as it was theirs it was still having some effect on her. Either the Angel couldn't penetrate deeply enough into her mind or it was afraid to, having noticed that her mind was not as easy to access as theirs had been. It seemed though that it hadn't realized just whose mind it was trying to enter. Even at that she was seeing things that had been dredged up from the depths of what could only be her own memory, memories that had eluded her recall with the damage done to her from the tearing apart of her soul.

She saw magnificent cities of marble and crystal, perhaps the place where she had originated from. She felt pride at having been one of the special souls crafted by the ancients, the First sentient and evolved beings in the entire universe, beings that were ancient when this world was still a cooling ball of molten rock. Pride at being chosen to be a Seed and bring the wonder that was life to an otherwise lifeless world. She remembered her journey here, taken in wonder as she passed the few other worlds that contained intelligent life be it evolved or seeded.

Darker memories began to surface. The arrival of a second Seed, Adam, an event that should not have taken place. The First took great pains to ensure that such a thing never happened. Having two Seeds inhabit one world always led to conflict and that world's destruction. It was the result of a hard learned lesson from eons ago. Two seeds were never supposed to be sent to a single world and every Seed was accompanied by a Lance, a safety mechanism to seal or destroy them if they went rogue and disobeyed the edicts laid down by the First in regard to interfering in the lives of the beings the Seeds created and playing God with them.

But someone had disobeyed and had sent a second Seed to the Earth. It was a serious offence and the consequences would have been immediate when it was discovered. She also would have been informed of it by an emissary from the First, sent to investigate the situation as soon as they detected the problem, one of the very few reasons for one of the First to ever set foot on one of the seeded worlds before its denizens reached a certain level of evolution. A level that the people of this world would likely not see for thousands of years yet.

She actually let the Angel have just a bit more access in order to force out more of that particular memory. The one who had sent Adam. The one who had committed the crime of trying to infuse Seeds with the traits that both she and Adam possessed to create a being of both vast power and intelligence, an unstable mixture if their ever was one. The one that had tried to sabotage the seeding of this world had been brought here and stripped of all of his power and placed in a human body. A body that would see him age very slowly over many centuries until it finally failed.

His sentence was to observe the beings of this world and in an attempt to redeem himself, work towards improving and advancing the lives of the people in whatever way he could within the limitation of being one of them. Her eyes went wide as she realized the identity of that person, or at least the identity that he currently wore.

Lorenz Kiel.

She had already regained fragments of her memories regarding him and she had known that he played a significant role in things. She knew that he had indeed been around for centuries but she didn't know why or how he had been able to live for so long. There had always been something there just on the edges of her shattered and fragmented memories but no matter how hard she tried she had not been able to recall it until now.

A blinding pain shot through her head, feeling like something had broken or burst. Suddenly all of the memories that had been lost and fragmented with the tearing of her soul came rushing back and pieced themselves together, filling in the many blanks. A Seed, once life had been created and set upon its path, they would go into a sort of hibernation, asleep but still aware of its creations. Over the centuries she had lain dormant in the Geo-front she had been able to see the progress and failures of the species as a whole through that connection. From its greatest achievements to the sad inevitability of it warring with itself. All races as they evolved went through the same process. Some destroyed themselves utterly while some survived to continue to grow and evolve.

But there had been one being she had been a little more aware of that the rest. While his body and soul felt human to her, it was also obvious that there was something off about him. The man that became Lorenz Kiel had spent lifetimes roaming the world, investigating any sort of seemingly unnatural occurrences and seeking out artifacts from numerous civilizations. For centuries he moved behind the scenes, affecting events, building wealth and power that would carry from one identity to the next when it became necessary for him to supposedly 'die'.

She began to look at these memories more closely than she had over the centuries, looked at the things he had been doing. A pattern started to emerge and she began to become enraged. All along, all of the things that he had done for centuries was geared towards breaking his punishment, breaking the seals that restrained his evolved powers and abilities as one of the First. The blueprint for it, the relics that foretold of the coming of the Angels, the secret Dead Sea Scrolls...they had been written by him! He was the architect of this madness, a plan centuries in the making. He was going to use the destruction of the human race, her creations, her _children_ to undo his punishment and regain his power. He was the hand behind Second Impact, putting things in motion to sacrifice billions of people to set the stage for the return of Adam's children. Even before that he had been responsible through his schemes and deeds for an untold number of deaths.

In her hibernating state she couldn't interfere and wasn't allowed to even if she could. It was a strict edict of the First that a Seed couldn't influence either positively or negatively the beings it created. Once created it was up to them to sort themselves out, to learn, grow, and evolve.

There were some who didn't like that non interference mandate for various reasons but to actively go against it was a serious a crime. Like Kiel, they thought making the beings more powerful would ensure their survival and allow them to fend off more aggressive races they may encounter along their evolutionary path. But Kiel had only worsened his position by actively trying to sabotage a Seeding, then trying to completely subvert his punishment by using those seeded being's souls to free himself. Should an emissary return here again he would most certainly be executed after being taken from this world. She found it somewhat surprising that Second Impact hadn't brought one.

 _'Kiel,'_ she seethed. _'You have done this, you have nearly destroyed this world and my children. You are the one who has brought this pain and suffering.'_ She looked across the transition space, her guts, her very soul twisting at the sight of the anguish and torment Misato and Shinji were going through. _'Because of you they have suffered untold misery and hardship. You have taken their innocence and given them nothing but blood and pain in return.'_

Her attention turned back to the immediate threat of the Angel. She let her anger free and let her power rise, shaking off the effects of the attack and allowing the beast to come to the surface. Sending a burst of her own power back along the Angel's beam of light, she heard it shriek in surprise and pain and felt it falter.

 _"Now little Angel,"_ she growled menacingly. _"I will end you!"_

Unit 01, the Berserker, rose to its feet and roared deafeningly at the sky while six sets of orange wings fashioned from its AT Field sprouted from its back. The NERV staff was beyond speechless at this point and could only watch in awe and fear as the purple destroyer crouched then leaped and shot through the air. The resulting sonic boom blew out the windows of every building not lowered into the Geo-front and caused already damaged structures to collapse. It looped and spiralled around the Angel's light beam as it frantically tried to bring it to bear once more. Not that it would do much to Unit 01 or Lilith if it did, but she had Shinji and Misato to think about and if the Angel was still trying to pin them in its light then it wasn't trying to get away.

Unit 01 passed through the Angel's AT Field like it wasn't even there and made a four point landing, its hands and feet smashing into the Fifteenth's crystalline body. The Angel screeched in pain but with no appendages and its AT Field useless it couldn't shed its attacker. With a roar Unit 01 reared back and slammed both of its hands into the core, splintering it and tearing out two great handfuls of it, crushing them and them tossing them aside before going back for more. The Angel shrieked and screamed its death knell as the Berserker tore its core apart, not even giving it the opportunity to self destruct and try and take its attacker with it. Without the core, the body soon cracked and splintered apart, falling back to the earth and creating a light show as it burned up on entry.

Lilith used the time as she watched it fall and burn to regain her composure and check on her passengers. They were still clinging to one another and barely conscious now, weeping softly in their shared torment. For their own safety and her peace of mind she moved them from the transition space and into the core. She knew the ground staff would start freaking out because Shinji was within the core again but she was sure Yui could handle them. They needed the respite after the ordeal they had just endured and it would be quiet and peaceful for them there. Once she got them back to ground and inside the base she could help lessen the impact of them reliving each others worst memories.

She _could_ blank their memory of the incident but she was loathe to do so. Having a blank spot in their memory could cause problems of its own and it wouldn't help them deal with the root of the problem which was the old memories themselves. The Angel hadn't planted false memories in their minds or shown them visions it had conjured up, it had brought their own worst memories to the surface and they had shared each others as well. Individually their own memories would have been painful enough to relive again just as the day they had happened with all of the same emotion and sensory input of the time. But to relive the worst memories of someone else the same way as if they were your own, the memories of someone you held a great deal of affection for at that, it was doubly bad for the both of them. At some point they will have to deal with what they experienced in a way that would actually help them accept and overcome the trauma.

Rather than blanking the incident for them she could help ease the effects and allow their own minds time to process and deal with it without having everything feel like it was so stark and fresh to them. Dull them a little in a way like a local anaesthetic dulled the pain of a wound. The pain wouldn't go away entirely but it would be manageable and they wouldn't be overwhelmed by it as they sought to deal with the issues themselves that were the cause. Killing Gendo would be a good start but she supposed that was out of the question. It would eradicate a great deal of the cause, but would do little for the effects. She knew she would feel better for it though.

Predictably NERV was in quite an uproar as she brought them back down to earth. The Bastard King had issued all manner of commands concerning evaluating Unit 01 for potential contamination and she was content to let them do whatever they wished before they finally put the Eva back in its berth. She quickly relinquished control as soon as she set it down near one of the elevator platforms and had a few words with Yui before joining her partners in the core.

She found them laying on the beach of the core's inner world, still wrapped in each others arms and now asleep. Hopefully peacefully so. Shinji was mostly laying on top of Misato with her breasts providing him with a comfy pillow. If he had known or been inclined to move, Misato wasn't about to let him. Both of her arms were wrapped around him and her left leg was hooked around his right. Poor boy might have a heart attack if he knew the position he was currently in. She sent a mental image to Yui, knowing that she would enjoy this. Her mirth was tempered though as she drew closer and could see tears still escaping from their eyes.

How much more would he, would either of them have to endure before it was all over? Could they? Could they hold up under any more strain after everything they had suffered already? All of their pain, everything the people of this world had been forced to endure was due to the machinations of one man. The race that created her had much to apologize for. There should have been someone watching what Kiel was up to for so many years but it seems that no one had. The two souls before her were owed that much at the very least if not more for having to be at the sharp end of this fight to stop what that man had put into place.

She laid down next to them and draped her arm over Shinji's back and began to let her otherworldly energies bathe him and Misato and dull their pain. She would do everything she could for them both now and in the future. Just as she would for Yui, just as she would for Rei. And she supposed just as she would for Asuka if the girl had truly purged herself of that disagreeable side of herself. She too was a victim just like all the others were but it was inexcusable to her for the girl to have made victims of others just to placate her sense of self importance so that she could mask her own misery.

But that was an issue for another day. Right now she just wanted to settle in with these two and help them if she could and get a little rest herself. Letting that berserker state out and keeping it under some level of control was tiring even for her. Maybe if she put enough effort into it she could set all three of them up for a more pleasant dream than the one they were currently having. With the three of them sharing some skin in a setting like this it would make for a nice one and they could all use such a pleasant distraction after the horrors of the day.

* * *

 _ **Later, Cage Observation Room:**_

Normally when a full diagnostic was being run on an Evangelion, Ritsuko Akagi would often tend to other business unless something about the testing required her direct input or supervision. Maya and the others were perfectly capable of running the tests, her main contribution was to interpret the data afterwards. After the exhaustive testing for contamination they finally started the diagnostic run with an extra careful eye on monitoring the core for any fluctuations or abnormalities, no mater how small or insignificant they may seem. With Shinji trapped inside the core again nothing could be overlooked.

Yui had assured her that Shinji was fine. She wouldn't elaborate and that had Ritsuko concerned. She couldn't understand how she could seem so unconcerned when her son was stuck within the core again. There was something going on here that she couldn't begin to figure out. However, that didn't mean that she had worked up the courage to confront the woman over it or to even just converse with her beyond what occurred the night they crossed paths in Rei's ICU room.

Really though, what did she have to lose? What was the worst that could come out of it? Yui had to know by now about her involvement in things and about her relationship with Gendo. Though she doubted she would be upset about that considering she seemed to have no positive feelings left for him. She couldn't feel much lower than she did right now, couldn't _get_ much lower than she already was. She was really beginning to truly understand the level of self loathing that Misato suffered from, she was buried up to her neck in it right now herself.

When Yui decided to set up shop in the observation room so she could keep an eye on the Eva while she went through the brainwave logs from the attack, particularly from the point of the Eva going berserk, she tagged along and worked from another console there. Few words passed between them, just greetings of courtesy and a word or two about what they were working on. She had even fired up the coffee maker in the back of the room and offered the other woman a cup, which she was grateful for, but her idea of using that as a way to break the ice and start the serious conversation she knew that they would have to have at some point failed when her nerve did.

So, for the past hour and a half they had both went about their business, though to be fair Yui seemed to be far more engrossed in her work than she was. Her eyes kept straying to the other woman and several times she went to speak, but words failed her every time. She couldn't even seem to find her voice to ask anything of a technical variety. She was so emotionally ransacked that she couldn't even muster up the strength and resolve to do that much.

"I won't bite you know," Yui's kind voice spoke, interrupting her self pity. "Especially now that I no longer can control the Eva." She smiled. "I'm not nearly as intimidating now."

She almost smiled at the joke. "I'm sorry," she apologized. "I've wanted to approach you but my courage left me every time I tried."

"If this is about Gendo then you have nothing to worry about," Yui assured her. "If anything you have my condolences for being yet another of his victims."

Ritsuko sighed. Consequences be damned, she had to, needed to talk and be honest. "I think there is some small part of me somewhere that knew right from the start that I was just being used. I had never been good with relationships, always had my head stuck in a text book. I was lonely and he was someone powerful and was working on things on the cutting edge of science. And I wanted to surpass my mother and what better way than to do that than take over and improve upon her work and take the man she had given herself to as well. I didn't even consider how tacky it was at the time that he told me that he needed me with him at my mother's funeral."

"What!" Yui bristled, unintentionally making Ritsuko flinch. "I'm sorry, I didn't mean to startle you. I always thought Naoko was after him, but for him to proposition you at her funeral...that bastard has no concept of shame!"

"Apparently neither do I," Ritsuko continued quietly. "I let my need to be wanted blind myself to the things I was doing. I was more than willing to flush humanity down the drain in exchange for being loved and wanted. But by the time that I realized that love was one sided and that I was nothing more than a tool to him, it was too late. I was caught in the web and there was no getting out. So I just kept on being his sex toy and kept trying to fool myself into believing that he actually cared. The only thing he actually cared about all along was you and his grand scheme to be with you again."

Yui pushed her computer monitor aside. "When I first met him I thought I could redeem him somehow, turn him away from the thug that everyone saw him to be. Make him care about the world that he felt cared nothing for him." She shook her head sadly. "Everyone said he was no good and they were right. The only good thing to come from my relationship with him was Shinji and he has done untold damage to him." Her eyes took on a hard look. "For that alone there is no forgiveness to be had."

Ritsuko sank wearily into her chair. "And I was a part of it. I helped to pressure him into the pilot's seat and did nothing to help make things any better for him." She lowered her head in shame. "Not for any of them and I treated Rei the worst of them all. I was so starved for Gendo's attention that I begrudged her every second of it that she got, even though I knew what her role was."

"I am well aware of all of this," Yui said, her voice taking on an icy tone that made Ritsuko sink lower in her chair and sent a shiver of fear down her spine. "All three pilots have sat in Unit 01's plug and I have seen memories from all of them. Believe me when I say that I am not happy about any of it."

She may no longer be within the Eva, but there was very much an angry Evangelion vibe to her words. A seriously hard, cold and pissed off vibe with a side of looming judgment and punishment.

"There isn't a single thing I can say in my defence," Ritsuko admitted quietly, feeling very much like the executioner's blade was at her neck. "There is nothing that I can offer that wouldn't sound like an excuse."

Realizing how she sounded, Yui sighed and closed her eyes for a moment, calming herself. "It's not like I can claim any moral high ground myself when I left my own son to this fate. I foolishly believed in the Instrumentality project back then and allowed the thrill of being far out on the leading edge of science to overcome my sense of humanity. I was doing it for my son's future and I was so wrapped up in it that I couldn't even see how I was going to damage him by letting the Eva take me and ensuring that he would be its pilot. Talk about being backwards, I was trying to save my son and his future by sending him to war. I left him right in Gendo's hands for him to do what he did. Gendo may have done the deeds, but I made it possible." She took a deep breath and let it out slowly. "And yet, Shinji refuses to blame me for what I've done."

"What changed your mind about Instrumentality?" Ritsuko asked, genuinely curious.

"Time to think about how absurd it was to believe that mankind's evolution had reached a dead end," Yui replied. "Realizing that Gendo was not following through and having Shinji train here and sync with the Eva. Most of all though I learned that things weren't as they seemed to be and its purpose was not what SEELE was selling to its cabal of true believers. The picture was incomplete until now, but what I learned was more than enough to know what a colossal mistake this was."

That got Ritsuko's attention. "Wait a minute, how could you possibly have learned anything when you have been in the Eva's core for the last ten years?!"

"Before I answer that, let me ask you a question. Your answer will determine whether or not you get one from me." She intently looked Ritsuko dead in the eyes. "Do you want to stop what is going on and keep this world and all life on it from being destroyed? Gendo may be at a crossroads and does not yet know what direction he wants to go with this now, but even if he decides not to go through with it, SEELE will continue on regardless."

"Trying to sell me redemption?" Ritsuko scoffed.

"Hardly," Yui answered. "We are all well beyond that for what we've done. But we owe it to the rest of the world to stop this. If not for the world, I at least owe it to my son."

"If I say yes you will tell me everything?"

Yui nodded. "And I will expect your full cooperation. Say no and you get nothing."

"And if I don't cooperate?" she dared.

Yui gave her a dark look. "You'll mysteriously disappear without a trace until this is all over with and then you can fend for yourself in the aftermath."

Ritsuko blew out a long held breath. "You know, when you first came out of the Eva...hell it was before that even...I had been lamenting the mess I had made of my life and the even bigger mess I had gotten myself into. The conscience I thought to be long dead re-emerged and began nagging at me. I know that I should have tried to do something long ago to expose all of this but I was a coward who caved in to her weaknesses and jumped into hell with both feet despite knowing how wrong this was. You're right when you say that there is no redemption for what we've done but I've already taken the easy way out of things. For once, I would rather stand up and do something right even if it means living with what I've done for the rest of my life. Bearing that shame is as close to redemption as I will ever get. So yes, I want to stop Instrumentality from ever happening."

Yui smirked. "Get comfortable then, because this will take a while and will probably blow your mind."

* * *

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	15. Chapter 15

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

 **Transposed**

 _ **Chapter 15**_

 _ **Asuka**_

It was becoming painfully apparent to Asuka just how much her reputation tended to proceed her. She had always suspected that because of her brash, aggressively self centred ways that there were many among the staff of the various departments of NERV that were not fond of her. Some who were more familiar with her may have developed and outright but quiet hatred. However little was ever said since it was well known that messing with the pilots in any way was generally looked upon with great disdain by the Commander and no one with any sense wanted to get on the wrong side of him.

That didn't mean that certain members of the hospital staff didn't view her with disdain or outright disgust, notions gained from that previous behaviour. The doctors were fine as were most of the older staff members. They had more than enough experience with mental illnesses and its potential causes to be more understanding. Obviously they had been made aware of her full past history and could already formulate the aspects of her condition. Some of the younger ones on the staff and those who weren't privy to her history were less understanding and many of them were fearful that the end was only a matter of time with NERV's fighting strength down to only one pilot and the cause of that problem was housed right in their midst. Their displeasure was made known to her today.

She had certainly heard the alarms go off signifying an Angel attack, and had spent the duration of the alert huddled on her bed shaking like a leaf. The Angels had kept getting stronger each time and the only thing standing between this latest one and the end of the world was Shinji. She well knew as did everyone else by this point that conventional weapons would do nothing. The only weapon against them was the Evangelion and right now there was only one that had a pilot capable of fighting. She knew full well that she was responsible for it and that if things went all to hell, she would be to blame. Of course, there wouldn't be anyone left if that happened but she would die knowing that her actions had doomed mankind.

She, or at least that other part of herself, had always ridiculed Shinji by calling him 'Invincible Shinji', or worse, the 'Invincible Baka'. As she lay trembling in her hospital bed waiting for either oblivion or the all clear, she had hoped beyond all hope that Shinji really was invincible. She hoped that he would win and that he would come out of the battle unscathed. She was having a hard enough time living with what she had done and she didn't think she could take it if he were to be seriously hurt.

Once the all clear had sounded and thankfully lifted the weight of the world off of her a little, she was allowed to leave her room and go back out to the windows overlooking the Geo-front. The doctors had decided that it would do her good to be allowed out of her room and have something to look at other than four stark white walls. It was where she had been when the alert sounded and she was glad to be allowed to go back for a while again. While some of the landscape visible to her bore some scars from the battle against the Fourteenth, the view was indeed still better than the inside of her room and it made her feel a little better.

She sat there once again feeling a great deal of relief that the Angel had obviously been defeated and hoping that Shinji was alright. Not far from her a couple of young orderlies and nurses were discussing the attack and what they had heard about it. She couldn't catch every word, but the gist of it was that the Angel attacked from orbit hitting Unit 01 with some kind of a light beam, Unit 01 went berserk and somehow flew up and killed the Angel and now Shinji was once again stuck inside the core. Unless she heard wrong they also said something about Ayanami literally crawling to her Eva to try and go help him, but being unable to get into the fight.

She could feel their eyes glaring at her and could hear the bitter accusation in their voices. As far as they were concerned she had doomed them all. All three pilots were now out of commission and unless Shinji reappeared again before the next Angel came or Ayanami recovered enough to pilot, they were done for. She tried to tune them out, she didn't need to hear their words to know what she had done and the position she had left them all in. She was all too well aware of it because the thought refused to leave her head be she awake or asleep. How was she supposed to cope with that knowledge? How was she supposed to cope with the illusion that was her life, knowing that because she couldn't keep herself together that she had potentially doomed humankind? Was this how it was to be? She was finally free of that spiteful, hate filled part of herself but in its final act it had possibly doomed them all. It was her fault. She had let it grow and rule her life in her place. Her weakness had done this.

When she had found her Mama and the doll that was supposed to be her hanging from the ceiling of the hospital room, it had taken surprisingly little time for that other side of herself to manifest and begin to grow. Eva had split her mother's soul, leaving the worst part of her to inhabit her body. Finding her body had split her mind and left the worst aspects of herself in control. It hadn't been clear to her before just exactly when her split had really happened. Now she knew. The day she found her mother was when the split occurred, but it wasn't until she came to Japan that the side of her that was in control ever began to notice it and hear the other voice within her.

At the root of it all, she supposed she had always had a big ego even at such a young age considering how everyone fawned over her and told her how special and talented she was. The harder she trained, the harder she worked academically, the more praise she got for her accomplishments and being so driven and so busy kept her from thinking of that day she found her Mama dead. It wasn't long before she felt she was so deserving of all of that attention that she began to react badly when she didn't get it, or when it looked like someone else was outshining her.

She hadn't cared how badly she treated others, hadn't cared what they thought of her. She could justify all of it in her own mind. Others were beneath her and they were just jealous that they couldn't be what she was. She was brilliant, she was beautiful, and with her exceptional skills she was going to save the world all by herself. No one would be able to match her in any regard and especially not an emotionless doll and some weak little boy. This fight was what she was born for and she didn't need anyone riding on her coat tails and tagging along. She didn't need them and she was damn well going to make sure they knew it.

What a damn self centred, egotistical fool she had been. She fancied herself the irresistible force but reality was the immovable object that she had no hope of overcoming. She had been tested and found severely wanting. There wasn't one battle that she had won on her own and she had considered every one of them a failure. She was supposed to be the best pilot with the best Eva and all of the glory should have been hers. She never learned the lesson that glory didn't matter when you were fighting for your life, only the end result was important. Instead of being thankful at the defeat of each Angel she instead got angrier and angrier that the spotlight wasn't fixed solely on her, cursing her fellow pilots for what she saw as their interference in her fight and having to be saved like a damsel in distress by Shinji and being robbed of even the honour of a warrior's death.

And all the while, the true part of herself, the scared little girl that had to watch what was left of her Mama's mind disintegrate until she found her hanging from the ceiling, sat huddled alone in the cold darkness unable to do anything as the disagreeable thing that she had become brought them closer to oblivion. All she wanted was someone to hold her and tell her that they cared, that it would be okay and things would get better. But she was an unwelcome passenger on a ride she never wanted to take, buried so deeply under the pain and anger that she thought she would never see daylight again.

When she finally did emerge again it was into the harsh light of the consequences and the hatred from what that other part of herself had done. Everything behind her was scorched earth, there was no forgiveness to be had and no redemption forthcoming. The spotlight was truly on her now but for all the wrong reasons. She hated that other part of herself for leaving her this mess to inherit, but she hated herself even more for not being able to do anything to ever prevent it from happening. She had cowered in her dark little prison and let that other part have control and never fought to take it back. At best all she could ever do was try to make her voice heard now and then in a desperate and futile attempt to make the other half see reason. In the end all she really did was make it worse and helped to push that other part of herself completely over the edge.

The anger, the sheer fury...it had been terrible and had torn at her mind, threatening to rip her to shreds and blow her away into nothingness. It had been so hard to hang on and not disappear but every second that passed felt like she was being eroded away bit by bit by the maelstrom. She had begged and pleaded for it to stop, screamed and cried in terror as the storm raged. When it finally ended there was nothing left of her other side and very little left of her. She was little more than a ragged presence when she staggered up to Shinji. It all hurt so much and she was so confused. What had been done in the midst of that rage darted about in her mind like pieces of a jigsaw puzzle being tossed about in a gale, all jumbled and out of place and she could still hear herself screaming and crying.

It was like that every time she nodded off into sleep or even came close to it and it was threatening to encroach on her conscious mind now as one of the orderlies was yelling at her, something about her not having the right to cry after what she had done. She hadn't even realized she was crying but her fingers came away wet when she touched her cheek. Maybe she didn't deserve to cry, her tears certainly weren't going to help Rei or Shinji and they certainly weren't going to do anything to stop another Angel from arriving. But right at this moment it was all she had and all she could do. Couldn't she at least be allowed to cry and rid herself of the tears she had accumulated over the years and never allowed herself to shed? Couldn't she have even that one small concession?

She looked up and saw the wild, desperate look in the man's eyes, the look of someone who was fearing the end and wanted to take it out on someone both verbally and with the fist he was raising, despite his companion's attempts to now stop him. Maybe this is what she really deserved, to be beaten down like she had done to Rei, to be ridiculed and humiliated like she had kept doing to Shinji when all he had ever wanted was to be her friend and get along with her.

The blow caught her above the ear and sent her tumbling to the floor just as she heard her doctor shouting at her assailant. There was a great deal of yelling and scuffling going on. She became oblivious to it all as she curled into a ball and cried like she never had before in her life.

* * *

 _ **Ritsuko's Office, Several Hours Later:**_

 _'Life can be such a cruel bitch,'_ Ritsuko thought to herself as she leaned back wearily in the chair at her desk. But then again, she was pretty much the author of her own misfortune so she had little room to complain about it. Her newly returned conscience was making sure that she never forgot the things that she had done and been a part of and was making sure that she suffered the guilt for it. Somehow, she would have to deal with the guilt for what she had done as equally as for the things she hadn't but should have. She at least had a chance to make up for some of that now thanks to Yui Ikari, but her actions should have been hers alone to deal with without an otherwise innocent soul getting pulled into the muck with her. The fact that Maya Ibuki was currently asleep on her office couch was proof of that concept going all to hell and adding one more layer of guilt to her already overburdened soul.

Just after she had accepted Yui's offer and the woman had begun to fill her in they had heard a noise outside the door. Yui hadn't seemed surprised to find Maya there and she couldn't help but wonder if she had known that her assistant had been there and heard nearly everything they had said up to that point. She had brought the results of the diagnostic checks to give to her but hadn't wanted to interrupt their conversation and proceeded to hear some ugly truths. She hadn't really wanted Maya to hear anything more but Yui had other ideas. The cat was already out of the bag she had said, and Maya might as well hear the whole story and could decide for herself how much faith she wanted to retain in the woman she looked up to so much.

Somewhat cruel to both of them, but she supposed it was better than Maya only having part of the story and even though she was young and somewhat naive, she wasn't a child and she wasn't stupid. She was capable of making up her own mind about the HIP and their reasons for having been involved with it. Even so, it wasn't easy to admit to Maya the things she had done. She didn't tell her everything but she told her enough to know that her beloved Sempai was no saint and was up to her neck in blood and filth. She wasn't sure though what had been worse, telling her what she had done or admitting to how she got mixed up in it in the first place and showing how truly weak and pathetic she really was.

She sighed as she looked at her assistant's face, still troubled looking even in sleep. Predictably, it had taken her a while to recognize that Maya looked up to her so much. Interpersonal relationships had never been her thing and when she tended to always be buried in her work it was little wonder she had gone as long as she had without recognizing it. Last night she had begun to get an indication of just how deep Maya's admiration and feelings about her really may have been when every revelation left the poor girl looking more and more crushed.

To her credit though, she didn't completely break down into a sobbing, broken heap. She heard them both out, listened to their stories and how they became involved in the HIP and why they did the things that they did. And she also listened in shock as they admonished themselves for how stupid and short sighted they had been in doing so and got a good indication of the heavy guilt they were both carrying.

Finding out the story behind Unit 01 had been a shocker of a different kind for both of them and left them speechless. The consciousness within was Lilith...and the truth of what Lilith was and the plotting by SEELE...in the end that was the last straw and a very stressful few hours finally caught up to Maya and she fainted. Hell, it had almost been enough to put her down too. Needless to say she didn't want Maya to wake up alone after hearing all that she had. Even if she hated her now for what she knew, her renewed conscience wouldn't let her leave Maya alone even though she had agreed to help put an end to all of this.

In a way she wanted to be mad at Yui for making Maya hear all of this, but again she had little room to talk. How many tasks had she given to Maya that helped forward the agenda even if indirectly? Even having Maya do some of her duties while she tended to some of the more nefarious projects Commander Ikari had her working on had brought the girl too close to the rotten heart of things.

Truth be told she had grown rather fond of her protégé. She was good at her job and eager to help and to learn and after she had finally realized that Maya practically idolized her she came to find it kind of cute. In her more quiet and reflective moments she had found it flattering how much Maya seemed to worry about her, concerned about the ridiculous hours she put in and her missing of meals and lack of sleep. When had the last time been that someone had actually worried about her like that? When was the last time someone had really cared about her?

She supposed it was those realizations that had actually started to help kick start her conscience back to life. As she began to admit to herself more and more how little Gendo truly cared for her, she saw in Maya someone who actually did, someone who always greeted her with a smile and was always happy to see her. Her cheerful kindness, if not naive innocence, could always make her smile and because of it she began to see just how truly guilty and filthy she was by comparison. During her years in college and the many social failures she had endured, most of those were the exact traits she had desired to find in someone. Gendo had been anything but that, but by that time she had been desperate for someone to love her and recognize that she could exist outside the shadow of her mother's achievements. When Gendo tossed her the bait, she swallowed it whole.

Yeah, that had worked out real well hadn't it?

She had heard the rumours and gossip going around, people speculating that she and Maya were in a relationship. She used to get a laugh out of it and as jaded as she was now she would sometimes turn the tables on the gossipers by asking them what business it was of theirs if they were. She had become an intimidating enough presence that people had learned that it wasn't a good idea to get on her bad side. Maya however she knew was stung by the gossip and rumours but there was something in the nature of her denials that made her think that the younger girl wasn't against the idea.

Truthfully, she hadn't even really thought much about it until recently as she had started take stock of her life. Would it be so bad if the true love and affection she craved so badly came from a woman? She didn't know how much of her heart was left after the use and abuse she received from Gendo but it seemed that there was still enough there that she wanted to be able to give it to someone who would cherish it and keep it alive. Perhaps it was little more than the remnants of a foolish dream. But if that happened to be someone like Maya, could she do it? She was afraid to open herself up like that again and she would have to be sure of the other person before she could ever even try. She doubted she could survive having her heart crushed for a second time.

Of course, after the things that Maya had just learned about her it may well all be a dead issue now anyway. There was no way that she would be able to look at her the same way now after hearing all of that and knowing that there was more that she hadn't been told. That one little bright spot in her life might be irrevocably dimmed now and ultimately she had no one to blame for it but herself.

Tears began to flow from her eyes. She brushed her right cheek with her fingers and stared at the salty fluid almost like she didn't know what she was seeing. She definitely couldn't believe it.

"All of the things that I have done and all of the humiliations I have brought myself to and not once did I shed a tear over it," she said shakily as she looked to the girl lying on her couch. "But now here they are and all because I fear her disappointment in me."

She tried to stifle them, to make them stop, but the harder she tried the more they seemed to defy her and the more they came. She began to tremble and shake, feeling very much like she was crumbling in on herself. The walls she had been constructing for so long to shield herself from the horrors of the work she was doing, the barriers she built up to protect herself from the lies she told herself about her relationship with Gendo...they were all falling apart and into a deep black abyss that was threatening to suck in her soul and her sanity as well.

She buried her face in her hands and tried to silence the sobs that now came. She felt so broken and she didn't know if she was even entitled to these tears. She was both a victim and a victimizer and she couldn't say that she didn't deserve this pain for what she had done but she also couldn't help but ask herself why it had to ever be this way to begin with. Why hadn't she seen sense and reason when she became aware of the sheer madness of what was going on here? Why couldn't she see past her loneliness and ambition to see the sheer insanity she was involving herself in? Look where it had brought her, look what she had gained for it all.

"Sempai?" Maya's shaky voice called to her.

She cringed and cried harder. She didn't want her to see this, to see her crying like she had a right to feel this way when she clearly felt that she didn't. She felt Maya's shaking hands gently grasp her wrists, urging her to lift her head up and look at her. She didn't want to, she was too afraid of what she would see in her eyes if she did.

"Sempai...please."

She finally relented and let her pull her hands away. Maya was kneeling before her and her gentle eyes were brimming with tears that were already trailing down her cheeks. She looked tired and definitely like she was still hurt by the truth, but there was also still a tinge of hope that always seemed to be there, like there was still a bright side to be seen in all of this. She had lost that kind of optimism herself long ago.

"I'm sorry Maya." She took a shuddering breath. "I'm not the person you believed in so much. The things I've done are indefensible."

"You were being used like so many others were," Maya countered. "If you hadn't done what he wanted he might have killed you."

She didn't want to believe the things she had been told, didn't want to believe that the people that she thought were leading them through this struggle had actually been pushing such a horrible agenda of their own. But refusing to believe it would make her terribly naive. She had seen enough on her own to know that things were probably not as they had seemed, but she had conveniently stuck her head in the sand and placed blind faith in those above her. It had been the easiest way to keep fear from gnawing away at her until there was nothing left of her.

"That doesn't make me blameless," Ritsuko sniffled. "So much of the work I did had one purpose and that was to bring us all closer to the end. My need to be noticed and loved doesn't excuse that. My needs are not as important as the survival of the world but I acted as if they were."

"But you're going to change that now aren't you Sempai? Maya asked hopefully, her hands now gripping her mentor's. "I can't say that I fully understand what drove you and I don't know if I even fully understand everything I just learned. It's just too much all at once. But you agreed to help Dr. Ikari end this and put a stop to the Commander and to SEELE. That has to mean something doesn't it?"

"Maybe it does," Ritsuko admitted. "But it isn't going to balance the scales. It's...I'm too far along for that." She gave Maya's hands a gentle squeeze. "Why aren't you damning me for my actions and for being such a pathetic and wretched human being? The face I've been showing you all this time isn't the real one, it wasn't the real me."

"You're wrong Sempai," Maya cried. "I think that face was the real one. The face of the person I've worked closely with and learned so much from. We've spent a lot of long hours with just the two of us working together. I've seen your different moods and we talked about normal everyday things besides just our work. I've seen you smile and be kind and I know you're not some inhuman monster. I've known for a long time that there was something that was hurting you, something that was weighing heavily on you but I never knew what."

"And now that you do know look what it has done to you," Ritsuko said, a fresh stream of tears leaking from her eyes. "I can see in your face and in your eyes that what you learned about me is hurting you."

"And that is on me," Maya countered. "It's my fault because I was acting like some teenager around their idol. I'm ashamed of it because when you idolize someone that much you put unrealistic expectations on them. You forget that they are human just like everyone else and I am sorry for doing that to you."

The wrongness of her idol worship was not something she had just realized after the things she learned last night. It was something that she had been seeing in herself more and more lately. The harder and more desperate things had gotten around NERV as the Angels kept coming had made her want to cling to the things she saw as solid and stable and reassuring and that included her idolization of Dr. Akagi. But she had seen the cracks forming on the woman, had seen the toll things were taking and it made her waver in her ideals about her.

She was capable of cracking under the strain just like everyone else. She wasn't infallible, she could crack and break and fall apart and she could do questionable things and be irrational. The perfection one perceived through the practice of idolization was just as big of a myth as the idea that perfection even existed in the first place. It wasn't fair to the one being idolized and bordered more on obsession that any true feelings of love or respect.

It was during these realizations that Maya began to see her mentor as the human being she was and not an object to be idolized. She did look up to the woman, very much so. She was a brilliant scientist and she had learned so much from her already. She had become a trusted assistant to her and they had become friends. And somewhere along the line Maya began to realize that she actually had some pretty deep feelings for Ritsuko Akagi that were far deeper than the superficial nature of her previous idol worship.

Ritsuko smiled sadly. "That's probably the least offensive thing I've experienced in years. And if I had had such high expectations for myself I wouldn't have gotten into a mess like this in the first place. But I'm here now and there's no escaping it. I just didn't want to drag you down into it too."

"That's my fault too Sempai for listening outside the door," she chastised herself. "I got myself into this."

"You seem pretty determined to join me in the mud hole Maya," she sighed. "It's not a pleasant place to be."

"My faith in you may be shaken Sempai," she said sincerely, looking into her mentor's eyes. "But it's not broken. I still believe in you and you don't need to carry this alone. I might be scared, maybe too scared to be thinking straight, but I want to help. I want to help stop this and I want to help you."

Fresh tears welled up in her eyes. "This isn't quite the same as what the Sub Commander said about letting others help carry the load you know."

"It doesn't matter," she countered. "I'm still here anyway."

Ritsuko squeezed their still held hands and leaned forward until their heads touched. She could almost feel the heat rising off of Maya's face. "Thank you Maya. So long as there's at least one person who believes in me maybe I can find a way to live with myself and keep going."

Renewed tears came to Maya's eyes as well. "You're in luck then because I'm not going anywhere Sempai."

* * *

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	16. Chapter 16

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

 **Transposed**

 _ **Chapter 16**_

 _ **Estate of Lorenz Kiel:**_

In the many years and lifetimes he had lived on this world and through all of the plotting and planning, Lorenz Kiel had always maintained a level of calmness amid chaos even when others around him were panicking and losing their composure. He had been this way for long before he had even been stranded on this world, but it had been necessary for him to relearn such skills as he was forced to live among the less evolved creatures that inhabited it. If anything the lower status of these humans was more of a challenge than dealing with his own kind. They were less predictable in many ways, their method of thought and action less precise and calculated than his brethren.

Thus it had taken many years to get used to them and their ways, to see how they thought. He had to be careful in his dealings with them lest he be seen as too much of an outsider or drawing too much attention to himself because of his advanced knowledge that outstripped them by several hundred millennia. It had been harder than he thought. Despite their often benevolent nature his kind could be unintentionally aloof and ignorant of the ways of those less evolved than themselves. That was one reason they tried to limit contact with the beings on the worlds they seeded until they had evolved to a point where they were intellectually ready to accept their existence.

It was a policy that he never really agreed with. What was the point of seeding a world with life if you were going to ignore it, if you were going to leave it to fend for itself and hope that in the end it would turn out as you desired. If you weren't going to give it the guidance it needed or even the might to survive then what was the point in seeding a world in the first place?

Mistakes were made along the way and he had needed to silence many to keep himself from undue scrutiny. As his plans were built and refined he made sure not to repeat those mistakes. It had still been necessary from time to time to make certain individuals disappear but he became insulated from any fall out by the organizational structure he built around himself and by the use of misdirection and the application of sufficient, untraceable funding. There had been many challenges along the way but his ability to remain clam and patient had seen him through the rough spots. However it was being challenged severely once again with recent events.

It had taken a great deal of patience and tact, and even a little thunder to reign in the other members of the Committee after the death of Harold Connelly III. Despite the wealth and power of the members and the ruthless and cutthroat way many of them attained it, they had begun to act like beheaded chickens, flopping around blindly with no sense or ability to direct themselves. The UNIO's Special Investigation Service was getting dangerously close to several people that could lead them directly to members of the Committee. Closer than he had expected them to be. There had been raids on several less than legal operations run by certain members, something he had warned them about and he had cautioned them to remain as far removed from such operations as possible.

For the most part, it wouldn't matter if all of the members of the Committee wound up dead or jailed, but there was still one outstanding issue that they were required for and it was highly critical. The completion of the mass production Evangelions and helping to keep them under wraps until it was time to deploy them. He didn't have the time or the personnel in place to be able to take over control of those units himself so he had little choice but to continue to rely on the others. If they stayed on task and used their heads instead of panicking needlessly then things would stay on track and progress in a satisfactory manner.

With the Committee chickens back on their roosts for now there was another problem that needed his attention and it was straining his patience even more than they were. Unit 01 and its defeat of the latest Angel. The fact that it prevailed was good, but the way it did so was not. It should not have been capable of doing such a thing, projecting wings made of its AT Field. There was also the issue of the pilot's mind having been probed and affected by the Angel. It was imperative to know what had happened beyond the meagre reports his agents had supplied to him.

He had yet to contact Ikari but he knew he would not get what he required from that schemer. He didn't know what game the man was playing but he knew it was something he would not like. It was very troubling that the pilot was once again within the Eva's core and even if he was not he knew that trying to get Ikari to hand him over for questioning was unlikely to happen, doubly so now that the Child's mother was back among the living. He needed answers, more answers beyond whatever half truth's and lies he would get from Gendo.

Perhaps it was time that he had a talk with Yui Ikari herself. Mother and son both would be optimal, but he would take what he could get, when he could get it. The interrogation of the Child would have to wait obviously until he returned from the core once again, and he had a strong gut feeling that he would. He felt however that the most important thing right now was to find out what Yui Ikari could tell them about Unit 01 itself and why it was acting beyond predicted parameters.

Something was amiss and he was going to find out what.

* * *

 _ **Unit 01's Core:**_

Slowly, and with some discomfort, Misato's eyes opened to take in the pale blue sky above her. She didn't feel particularly great to say the least. Her head wasn't throbbing but ached dully and her eyes burned. Her entire body felt like she had been in a car wreck, she hurt and ached everywhere and she had little to no energy at all it seemed. Little wonder, the Angel's attack had taken everything she had, turned her inside out, devoured her and spit her back out. She was wrecked inside and out, but mostly on the inside.

The memories of what happened that day in Antarctica, the memories of every bad thing she had ever been through, they were always there. She had nightmares if she didn't drink enough before bed and memories were always hovering right there in her mind, but she had never had to relive them in such stark clarity and as if she was reliving them as if they were happening all over again with all of the requisite pain and mind numbing terror.

 _'But it wasn't just my memories,'_ she thought as she raised her head and looked at the boy sleeping with her chest as a pillow. The boy whose arms were wrapped around her just like hers were wrapped around him. Lilith lay next to them with her arm over Shinji's back.

She had seen his memories as well and lived the emotions attached to them as if it was happening to her. The crushing pain of losing his mother and being abandoned by his father. The years of neglect and the pervasive atmosphere of disdain from his guardians. The struggle of practically having to fend for himself at such a young age. The near total lack of anything that resembled warmth and caring from anyone around him. The crippling lack of self confidence and the ever deepening self loathing. The crushing loneliness. The screaming desire for someone to genuinely care about him and the desire to just simply disappear because it didn't seem to exist.

She felt his fear from the moment he came to Tokyo 3, saw the Angel, met his father and was forced to pilot Unit 01. She lived the struggle within him where he wanted to believe so much that she really wanted him in her home but feared it was only because he was needed as a pilot. She felt how he was hurt when some of the things she said and did squashed him time and again just when he was starting to warm up to her. The way she berated him after the Second Angel, the way she allowed Asuka to kick him out of his own room and run roughshod over him in what she had told him was his home and never doing anything to stop it. It made her feel ashamed of herself, made her feel like she had let him down. It had been obvious to her that he needed someone to help him learn to stand up in his life but instead she had left him to figure it out on his own and fend for himself. Not so different than the way his previous guardians treated him and that made her feel sick.

She also saw and felt that even though she had failed him time and again by turning a blind eye or not acting when she should have, he had still gained a great deal of affection for her and he had been terrified to learn that she had been hurt when the Angel had taken over Unit 03. She felt and lived his horror and rage when his father turned over control of Unit 01 to the Dummy Plug system and the Eva tore Unit 03 to pieces.

Damn the Angel that did this to them! It wasn't bad enough that Shinji had to relive all of that, but he had also had to relive her worst memories. The dysfunction of her family and the break up of her parent's marriage. The terror of being at ground zero for Second Impact and seeing Adam rise out of the frozen wastes. The years spent in silence and locked up within her own mind. Her own considerable self loathing and the way she whored herself out to Kaji. Her self hatred for her obsession with killing the Angels and using children to do it. He would even feel the deeper feelings she had for him and the way she felt herself to be so weak, pathetic, and disgusting for it.

She smiled weakly at his sleeping visage. In his own way he had shown her more care and kindness than any man ever had and he was still just a boy. Though, even as a boy and a fragile one at that, he was more of a man than most she had ever known. How many men would do what he did fighting the Angels, finding himself in the hospital too many times from it and enduring the pain of the Eva's wounds through synchronization?

Even so, to have such feelings for him couldn't possibly be normal or even remotely close to proper, right? There had to be something wrong with her, something in her head had snapped along the way with her wilful descent into self debasement. Or maybe it was because she had lost those years of her own life at the age he was at now and emotionally and maturity wise she had never caught up to her age. That somehow a part of her was still trapped in that time and filled with regrets for the type of life she could have had if things had been different. Maybe it was all of the above wrapped up into a tight little package of _'just how fucked up can I possibly be?'_

It didn't make it any easier now that she truly knew how he felt about her. Deep inside, so deep that even he could barely acknowledge it, Shinji loved her. Even with her teasing and her poor attempts to be a good guardian he thought she was beautiful, enjoyed being around her, and he felt genuine affection for her. He was scared to death of the idea of losing her or being torn away from her and she couldn't say that her feelings were much different.

It was much to her surprise to suddenly realize and understand that while they were under the influence of the Angel's attack and still connected as they had been, that even upon seeing all of the horrible truths of her life his feelings about her hadn't wavered one bit. He hadn't been disgusted by the way she debased herself, didn't think her vile or horrid for using him and his fellow pilots to gain her revenge against the Angels. If anything it seemed like he actually understood and identified with it all. For all of it there was a bit of sadness there, maybe even pity, and maybe even just a considerable amount both of anger and shame that she had been hurt so much by the events of her life, and in particular in being used by his Father.

She closed her eyes as tears began to leak from them once again. "You're too damn good for someone like me Shinji," she said in a barely heard whisper. "How can you not despise me for what I've helped to put you through, for what I've done to myself and for the feelings I have for you? How can you feel the way you do about me with all of that?"

"How could he not?" Lilith whispered in her ear. "You are the only one in ten years who has shown him any kind of concern or affection and you both needed someone to chase away your loneliness before it consumed you."

"I'm twice his age," Misato said sadly. "And I've made such a mess of myself and my life. I've used him just like everyone else."

"And yet he does not care and loves you anyway," Lilith countered. "Why do you deny what I know you can feel from him? What you know he can feel from you? Are you determined to remain alone and crush both of your hearts in the process?"

"He has others he cares about besides me," she cried. "He wouldn't be alone."

"No he wouldn't," Lilith agreed. "And I am determined to see that he isn't. I would see him surrounded by all those he cares for, no matter how many that may be because he deserves it. For everything that he has had to endure and for everything he has been put through in this war he deserves no less than every scrap of love and affection that can be given to him."

"He does," Misato agreed. "But he deserves better than what I am, what he has seen of me."

She regarded Misato with a critical eye. "If you think you can play the role of martyr here you are badly mistaken and I believe you know exactly what trying to do so will do to you. Age, the mess your life is, having others...all excuses to hide the truth that you are too afraid to be with someone who you know will truly love you, just like you have always wanted and needed someone to do. The mind lies and make excuses Misato, but the heart and the soul does not."

Despite knowing it to be the truth, it still hit Misato hard right between the eyes. She was afraid. As afraid of having the love she had desired for so long as she was of never finding it. But for all of the places for her to find it, it had to be in the heart of this boy. Someone who was half her age but at times twice as mature as she acted. Someone who should hate her for sending him out to fight and who should be disgusted by how she has lived. But the emotions she could feel from him through their connection were even stronger now than they had been before. If anything what he had seen of her worst memories had only made him reach deeper inside of her and hang on tighter and there was no doubting that she had wound her inner self tightly around him as well.

She badly wanted the love she was feeling so deeply from him. Wanted it and needed it. She needed it to survive and keep the world from drowning her, to keep from drowning herself in the misery that clung to her so stubbornly and that she seemed to be just as stubborn to not let go of. The truth of things was that when she got past the facade that was her disgust with herself at having these feelings for someone so much younger, she felt like she thought she would have when she was his age and if she had such feelings for someone. Having missed that part of her life she couldn't say if that was accurate, but that was how she imagined it and in the brief moments where she would allow herself to feel that before the self loathing took over again, it always felt right and gave her a brief moment of peace.

"It does scare me," she admitted. "But I guess I can't keep running from it anymore. If it's him maybe I can take the chance."

Lilith seemed greatly relieved. "You won't regret taking that chance Misato. It will be worth waiting for."

Shinji began to stir. His facial expressions and the groan he let out made it clear that he didn't feel much better than Misato had when she awoke. As he began to push himself up his eyes took in what he had been laying on, in particular where his head had been resting. The next thing to register was Misato looking at him with a small smile on her face and the fact that Shogoki was laying next to them. He then realized that all three of them were naked. Much to his shame he had to try quite hard to keep his eyes from straying to places he felt they probably shouldn't. The next thing he realized pretty much brought things to a full stop. They were lying on a beach at the water's edge and there was a small cottage further up from the shore.

"W-where are we?" he asked. He couldn't help the sense of panic that started to rise within in, especially after what he had just been through.

"We are inside the Eva's core," Shogoki answered. "It's alright Shinji, you are safe in here. And the Angel is dead so there is nothing to fear."

His eyes met Misato's, the recollection of everything that transpired flashing through his tired mind. If he wasn't feeling so tired and worn he might well have went straight to a state of panic, but something about the look in her brown eyes helped ease that. She had been through so much, even more than he had yet he always acted and felt like he was the only one to have things go so badly in their life. There were a lot of things about them that were the same, they both shared a lot of the same pain. It had hurt to see her worst memories and it hurt to see the way she showed her self loathing. But at least she kept trying where as he had tried to shrink away and hide from his life and the world.

If anything what they had gone through had only served to deepen the feelings he had for her yet he was ashamed of them. He was just a weak and timid boy who was always on the verge of just giving up, who hadn't been able to stand and even try to keep going forward like she had. To discover that she had similar feelings for him both elated him and filled him with trepidation. What did she see in him? She was an adult and he was just a scared kid and wasn't worth much. She saw how weak he had always been. Didn't she deserve something better than that, especially when she wasn't the only one he had feelings for?

"Misato, I-I'm sor..."

She cut him off by gently laying her hand on his cheek. "Don't say it Shinji. There isn't a thing in this world that you need to be apologizing for. Not a thing."

"Is it okay?" he asked shakily, tears forming in his eyes. "The way I feel..."

"It's fine Shinji," she assured him. "Because I feel the same way. I'm just as scared as you are about it but when all of this is over we'll work it out."

A look of relief lightened his expression a little. He turned to the dark skinned woman laying next to them. "The Angel didn't hurt you too did it Shogoki?"

She smiled at his concern, expecting nothing less from the soul she knew so well and adored so much. "No Shinji, but the attack did make me remember some important memories that had been lost to me. But that doesn't matter at the moment." That line of thought could lead to him learning who she really was and right now was not the time to drop that bomb on him. "What is, is how are you doing? You just went through something that was very traumatic and I can feel you shaking. Having all of your worst memories pulled up like that against your will had to be hard to bear."

He shook his head and if anything his body seemed to shake even worse. "It wasn't that. Those memories of my life are always there. They never really go away." He lowered his head. Tears began to drip from his eyes, splashing against Misato's chest. "That's why I always try to hide from them somehow but it doesn't really work so I'm used to them. But I-I saw all of M-Misato's bad memories too...a-and it was just like they were mine." He hitched back a sob. "It was like I was her...and I felt how much it hurt and how frightening it was...and how lonely she was..."

He broke down completely and a now crying Misato hugged him tightly to her. As much as it must have hurt him as he lived out those memories as if they were his own and with all of the sensory input to go with them, it seemed that the highest part of his pain and anguish was for Misato and not himself.

 _'This might be a good sign,'_ Lilith thought. _'If he is seeing it that way then he isn't taking it onto himself so much and adding to his own problems. This sort of attack could have caused their minds to collapse. Maybe because their minds were linked together at the time...and because they have strong feelings for each other...did that allow them to endure it?"_

That wasn't to say that she hadn't expected a breakdown from one or both of them, if anything she had feared that it would be far worse than this. The mind of a human was not strong enough or powerful enough to stand up under the onslaught of a higher being like one of Adam's children. Though perhaps it was fortunate that the Angels were more beings of power than intellect but that didn't make the latest attack any less brutal or any less painful.

Doubt began to creep into her mind as she watched them cry and cling to each other so desperately. Maybe she should have wiped the memory of this attack from their minds. Perhaps she should have tried to shield them better with her own mind even at the risk of exposing them too much to her own consciousness. They had already been abandoned, used, and abused enough in their lives, they should not have to endure the pain of having their worst memories pulled up by force and exposed to one another. Her sorrow for them and her rage for those responsible were in equal measure but neither of those emotions were going to help them. The only thing she could really do right now was wrap her arms around them both and let them know that they were not alone.

She also knew that she wouldn't be able to send Shinji back yet. Not until she was sure he was going to be alright and not before he and Misato had a chance to talk to each other a little more about what they had both seen. It was clear that how they felt about one another had not changed for the worse, but before either of them could go any further they needed to talk about their ordeal with each other...sort of a cleaning of wounds if you will. The best person for either of them to talk to now would be each other. No shrink in the world would be able to understand this trauma and find a method to deal with it. Not while it was this fresh and raw.

She would give them all the time they would need. They would be safe and undisturbed here and the environment was peaceful and relaxing. If they needed her assistance she would do whatever she could to help and in the meantime she would examine her own doubts and work her way through them. She was the foundation and the fortress they relied on to get through this war and she would not fail them, nor would she fail Yui and the trust she had placed in her. The Angels would die. Kiel would die and his sick plans would be ground into the dust. No other outcome was acceptable and she needed no further motivation than the weeping boy next to her. She would make their enemies pay for every tear he shed with their blood.

* * *

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	17. Chapter 17

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

 **Transposed**

 _ **Chapter 17**_

 _ **Office/Lab of Yui Ikari:**_

Reluctantly Yui gave up on any further attempt to remain asleep. The couch was comfy enough, that was why she had chosen it after all so many years ago when she outfitted her office. She knew there would likely be many nights were she would end up sleeping on it instead of at home in her bed so she might as well get one that fit the need. Luckily for her after being taken into the Eva, rather than cleaning out her office and lab they had simply removed any experiments, covered the furniture and locked the doors so it didn't take much to get settled back in now.

The fickleness of her sleep wasn't even due to the events of the last evening where she filled in Ristuko and her assistant on what was going on. Although she did feel a little bit bad about breaking Ibuki's image of her mentor, but NERV was a house of horrors and no amount of hand holding and coddling would do the girl any good. Ritsuko was going to need someone she could rely on to help keep her together and Maya Ibuki was already there and willing to fill the role. If Ritsuko now had to help hold her together too then so be it. It just might work out the best for them both that way.

The issue was that once again the anguish of her son was gnawing at her soul, fraying her nerves, and fuelling her self blame. Through Lilith she had witnessed what had been said between the three of them in the core. She wasn't sure what hurt more, hearing him say that he lived his own bad memories so much that he was used to it, or knowing that he was now feeling fresh pain from living the memories of someone he cared so much for. Again what hurt most of all was knowing that she was responsible for putting him on the path that led here. She was angry with herself, but was also equally as angry with Gendo for what he had done and put in motion as well as the mastermind of it all, Lorenz Kiel.

She was becoming frustrated as well. She wanted to be done with all of this so she could concentrate on reconnecting with Shinji and to help heal the deep and terrible wounds he carried and give him something that resembled a happy and enjoyable life. He certainly deserved that much at the very least. But there were still two Angels left to come and a number of other things that needed to be done before they ever came near that point. Hopefully one of those issues would be taken care of today.

She tossed back the blanket she had scrounged up for herself from the hospital ward and sat up, swinging her feet to the floor. It was at about that time that her still groggy mind realized that she was naked again, the sight of her clothes scattered on the floor before her in the dim light from a nearby desk lamp confirming it at the same moment. She couldn't remember if she took them off in her half awake state before she crashed for the night or of she had shed them some time during her restless sleep. At least this time she was by herself and hadn't walked out and into Shinji's view. She sighed. She had to do something about all of this guilt tripping she was doing. Every time she felt it she was in danger of slipping further down the slope and into the same kind of hole her son had been living in for most of his life.

While his troubles had been the product of the actions of others and he had no one to help him learn how to cope with it, everything she guilt tripped over had herself as the source. Even so, she couldn't keep hitting herself over the head for it. Shinji was already worried about her blaming herself for everything that befell him and she wouldn't be able to do much to help him if she drowned in her own guilt. She had already recognized and admitted just how much and how badly she had screwed up, now she needed to push that behind her and move forward and work towards building a new and better life for the two of them. She may never actually forgive herself for what she had done, but she would have to learn to live with it at the very least.

She looked at the clothes scattered about the floor, another set of hospital scrubs she had borrowed after the ones she had been wearing yesterday got soaked with LCL and Rei's blood. The injured girl should not have been able to awaken just yet let alone claw and drag herself all the way to the cages. Lilith hadn't done anything to force her awake, she had been occupied with the Angel's attack. The only other explanations were that it was a subconscious effect of having the same soul as Lilith and sensing something was wrong, or there was some other instinctive connection that Rei had gained for Shinji that told her he was in danger and being hurt. She couldn't say what it was but it was intriguing and she was impressed that Rei would go to the lengths she had to try and go help him.

Unfortunately she was in even worse shape now for it but if things went the way she hoped they would over the next couple of days she could give back what she had taken from the girl and then some. It would allow her to heal much faster and then she too could start forging a new path for herself. A path that perhaps would include a broadening relationship with her Shinji. She couldn't help but snicker. She new her son's feelings towards Rei and towards Misato and apparently those feelings were mutual. She also knew how Lilith felt about him so her love and affection starved boy may soon find himself swamped with what he had craved and needed for so long. Hopefully it wouldn't be too much too soon and she was pretty sure it wouldn't be. As damaged as they all were, none of the parties involved would have the capacity to move too quickly in this regard so she was sure it would all work out for the best. She was determined to make sure they all got the chance at least.

Rising from the couch she stretched and headed for the executive washroom attached to her office, and the modest shower within it. Another perk of her position and a necessity if she was spending nights on the couch and practically living out of her office. She had time enough for a quick clean up before hopefully finding something that resembled breakfast at the cafeteria before joining Ritsuko and Fuyutsuki for a meeting with Gendo. Talk about a horrid way to start one's day.

* * *

 _ **Later, Gendo's Office:**_

She sighed to herself as she took in the view of the Geo-front. Breakfast had been...typical of institutional fare, to be kind about it. But at least the coffee was decent and she had been sure to bring a large cup of it with her. She was pretty sure she didn't care if Gendo liked her doing that or not. It was interesting to see the ever so focused bastard have his attention divided for once though. While he was listening to Ritsuko's report about the state of Unit 01, which was perfectly fine with no signs of any sort of damage or contamination, she knew that he kept glancing at her. She was just beyond his effective peripheral vision so he actually had to move his head ever so slightly out of his usual pose. At least for once Ritsuko didn't have to feel like she was being stared down by a predator ready to rip out her throat at the smallest sign of his displeasure.

"This answers the viability of the unit itself, but what about the pilot?" Gendo asked when Ritsuko was finished.

Yui had to keep from snapping. The question may be a valid one, but the pilot did have a name. "Shinji will be back when she decides to let him come back," she answered.

"Are you referring to Major Katsuragi?" he asked her pointedly.

"She may have a role in it," she said as she approached the desk. "But I was referring to Unit 01's core consciousness. Nothing happens without it allowing it."

"What is going on with Unit 01 Yui," he demanded. "It was never supposed to gain this level of self awareness."

"You should know to never place limits and expectations on the unknown Gendo," she reminded him. "Especially with that particular unit. You know as well as I do that it was never a certainty that the growth of the Eva's consciousness was containable. The best we could hope for was to be able to contain its ability to act on its own will. The times that I was able to make the unit do as I wished only happened because the core consciousness agreed with my actions and allowed them, not because I was able to override its will."

"It should not have had a will of its own to begin with," he countered. "It was supposed to be a tool to be used as necessary and nothing more."

"And having a will of its own is counter to your scenario isn't it?" she jabbed. "Well I'm sorry dear but you can't always have what you want. You cannot bend Unit 01 to your will to fit your plans, whatever they may be now. It has evolved past what you could ever hope to control." Placing one hand on the desk, she leaned in to return his stare. "It does not have a mere consciousness, it has a fully formed soul. It is alive and intelligent and you should consider yourself very fortunate that after it landed from killing the last Angel that it didn't tear this base apart looking for you. She may well have if she wasn't more concerned for what Shinji and Misato had to go through while under the Angel's attack."

He looked stunned. "That...cannot be possible. How could it have manifested a soul?! That is not possible!"

She didn't even try to keep the amused look at his discomfort off of her face. "It didn't manifest a soul as much as it repaired and reformed a damaged one. That should be enough of a clue to give you the answer."

Fuyutsuki gasped. "Yui...you don't mean...Lilith?"

"Yes Professor, what is living inside Unit 01, specifically within its core is the Second Angel, the being that is the root of all human life on this planet." She looked back to Gendo. "Did you not ever wonder why Rei never showed any possible traits of Lilith's consciousness after you implanted her soul within her? For every hunk of flesh we carved from that giant body in Terminal Dogma to do our experiments for creating the Evangelion with, we were carving into her very soul. Even though she was in a form of hibernation the pain to her was excruciating and she could not escape it. Whether it was a survival mechanism, choice, or just pure dumb luck, the part that grew to become Unit 01 contained or redeveloped her consciousness."

"What you implanted into Rei was whatever was left of that soul," Ritsuko spoke up, rather enjoying the off balance look Gendo was wearing. "Whatever residue of Lilith's consciousness that remained was enough to allow Rei to form her own unique consciousness with no influence from Lilith's own."

Yui continued. "For some reason Lilith forgave me for my role in what was done to her. But you, for all of the people you have harmed, but most of all for what you have done to Shinji, there will be no forgiveness from her." She smiled darkly. "How does it feel Gendo to have a veritable demigod wanting to shed your blood?"

Gendo was nothing if not a resilient man. That ability had seen him through numerous encounters with the most powerful people on earth and had steadied him through revelations that would have left others paralyzed. However, the knowledge that Lilith was within Unit 01 and the spite filled delight that seemed to radiate form Yui in telling it to him left him momentarily stunned. Enough so that he never saw her lunge across the desk and jam a taser in his neck.

 _'I've always wanted to do that!'_ were the thoughts that simultaneously went through the minds of Akagi and Fuyutsuki.

Gendo's world went white and he convulsed painfully under the intense and unexpected shock. Part of that shock was indeed due to the taser, but there was no small amount of mental shock at the fact that it was Yui that had done it to him and she seemed to be enjoying it. By the time his faculties returned to him he was greeted with the sight of a smirking Ritsuko Akagi holding up an empty syringe and the sudden knowledge that he couldn't move his body.

"What...have you done," he said, struggling to talk through rapidly numbing lips.

Yui stepped into view. "We are taking your options away Gendo," she said icily. "You got what you wanted, you got me back but since it wasn't the great loving reunion you hoped for you can't seem to decide if you want to end this nightmare or perpetuate it." She leaned in closer. "I don't trust you to ever do the right thing so we are going to start dismantling your scenario and its many tentacles by removing that thing from your hand and destroying it. If you had ever had any intention or will to abandon your plans you would have done it already yourself."

Ritsuko pocketed the syringe and picked up Gendo's phone. "I'll send for the orderlies to come and pick him up then I'll oversee the removal."

"Yui..." Gendo pleaded weakly.

"Save it Gendo, you brought this on yourself," she told him. "When you're back on your feet you will still be the face of this facility, but you will be on a leash and you could try to gain at least some small measure of redemption by trying to do the right thing. Think of it as a new life experience since doing the right thing is something you have never tried before."

She went back to the windows and Fuyutsuki followed her. She had taken far too much delight in that. Maybe the exposure to Lilith's beastly nature before she regained herself had affected her more than she thought. She seemed perfectly capable now of inflicting a little misery when it suited her. Then again, maybe she was fighting fire with fire since the things Gendo had done had made him little more than a beast himself. Maybe it was just as simple as her loathing him that much now. Whatever it was it was obvious that she had changed. She went back to the windows and Fuyutsuki followed her.

"Sorry that I haven't told you everything Professor, but it had to be kept under wraps, at least until we could defang _him_."

He sighed. "Given my involvement thus far I have no room for complaints. So in essence Lilith is Unit 01. How did Shinji take that?"

"He doesn't know that part yet," she answered with a long exhale. "He has met her within the core and the transitional space between the core and the plug." He looked at her oddly. She smiled. "It's a space that could be best described as a common middle ground between the pilot's consciousness and the Eva's, or the soul in between like I was and Misato is now. Actually it may be more of a meeting of the actual souls themselves and becomes possible when synchronization approaches two hundred percent. Shinji met her during the first sync test with Misato. She just introduced herself as Shogoki, the consciousness of the Eva itself."

"I suppose it would have been too much on top of everything else he has learned and he's been through enough already," he surmised. "And now he's trapped in the core again."

"It's not a bad place and he has good company who will look after him," she said. "The Angel forced Shinji and Misato to see and relive all of their own worst memories as well as each others. Lilith wants to give him, both of them, time to calm down and gather themselves before she allows him to come back out."

He looked taken back. "Yui...are you able to speak with her, even here on the outside?"

She nodded. "Inside my head, yes. When I came out it was a one way connection. She left a part of herself with me to facilitate it but it had to be small to remain undetected. It wasn't until I borrowed a bit of her soul from Rei that I was able to make it work both ways. One of my next tasks will be to return what I borrowed but it will have to wait until Shinji comes back. We need the Eva to remove the Lance form Lilith's body so I can remove what residue of her soul that remains there and return it to her. Once I do, the flesh most likely will turn to LCL. If not, I expect that there is a method already in place by which the body can be destroyed if necessary?"

"There is," he admitted. "But without it there is nothing to draw the remaining Angels here."

"Lilith told me that Unit 01 should be sufficient for that at this stage and we plan on hunting the Sixteenth down if we can before it shows itself. She is sure that she can find it once her old body and the piece of Adam that Gendo has are destroyed. They provide a certain interference that keeps her from sensing the others before they emerge. As for the last one, if what you and Gendo theorize is true, it will come to us anyway when SEELE is ready to make their final move."

"We'll need to have a contingency for that," Fuyutsuki cautioned. "We also need to be ready for the possibility that SEELE will try and turn the government and other NERV facilities against us. Gendo may be a horrible bastard, but he did cover every possibility. His own private network of intelligence sources suggests that it is a very real possibility that we will end up isolated and under military attack. This base was never designed to repel an attack by human invaders."

"Kiel must have been considering that when SEELE, well GEHIRN at that time, oversaw the building of this base," she said. "It would not surprise me in the least considering how long he's been planning this."

"So what else don't I know?" he asked. "I assume their is something more to Kiel, judging by that statement."

"Indeed there is Professor," she admitted. "Let's go to my office. There are no unwanted eyes or ears there and quite frankly, Gendo's office gives me the creeps."

"Indeed it does," he agreed wholeheartedly as he followed his former student out of the accursed place.

* * *

 _ **Dr. Akagi's Office:**_

Maya Ibuki poured herself a cup of steaming brew from the coffee maker and seated herself at the spare desk she sometimes used when she was here. A quick shower at the women's locker room had made her feel a little better. It hadn't done much for the turmoil and post shock of everything she had learned, but it was a start and made her feel ready to get started with her day. She only wished she had a fresh uniform here after spending the night sleeping in the one she still wore.

Breakfast, such as it was, had reminded her why she usually avoided the cafeteria early in the morning. Lunch and even dinner normally wasn't too bad, but breakfast was not one of the kitchen staff's strong suits and was better off avoided unless there was no other alternative. Still, it had been better than having nothing to eat at all and it gave her stomach something else to do besides try and eat itself in a nervous fit.

The talk with Dr. Akagi earlier had helped settle her mind and nerves a bit. It certainly wasn't a cure all solution but it had cleared the air between them to a fair degree. Or if nothing else it had allowed them to carry on for a while now without breaking. There was too much to be done to stop what SEELE and their own Commander had put into motion so breakdowns and healing and redemption would have to get in line and wait their turn. Right now she had a task at hand that could help them thwart those plans.

Before she left to meet with the Commander, Dr. Akagi had explained a probable scenario to her. The upper command staff, meaning herself, the Commander, and Sub Commander, had reason to believe that at some point after the defeat of the Angels that SEELE would use the MAGI systems of the other NERV bases to attack and either disable or overtake the MAGI system here in Tokyo 3. Dr. Akagi already had a program ready to go, something she called a Triple Six firewall, but that would only buy them a limited amount of time. What was needed was a further way to protect the MAGI here. There were a couple of ways to do that.

One was to expand upon the Triple Six and bolster it somehow, the other option was to find a way to further slow down the attacking systems, hopefully by tying up their processing power at the source. Basically, Dr, Akagi wanted to find ways to hack the other MAGI and overburden them to the point that it would either slow them down in their attack, or possible prevent it altogether. Ideally, she would like to attack them instead and that was where she came in.

First and foremost, her job was to think of as many ways as possible to tie up the other MAGI systems, with the secondary objective of hacking them and giving them a virus to or two to take them down. The first key to accomplishing any of it was to find a way into the system. Some may see that as an impossible task given the sheer power of the MAGI systems and the security attached to them, and there was no shortage of reports of people who had tried and been prosecuted for trying. A direct hack of a MAGI system was almost impossible. If the other NERV bases attacked them together it could be done and that was the most likely way they would do it, confident that the Tokyo 3 system would be overpowered. That approach wouldn't work however for them to attack the others so it would have to be done through other avenues.

All of the MAGI systems essentially performed the same functions in their respective countries. They were the electronic brains of the NERV base and everything that went on there, but they also ran nearly all of the infrastructure of their home regions. The security on the MAGI systems themselves was daunting and the T-3 MAGI was probably the most secure of them all with the measures Dr. Akagi had programmed into it and constantly upgraded. But the soft spot was the other outside systems that were connected to it. Again, their own MAGI was probably less vulnerable to this, but the others weren't.

All software had holes in it, back doors left by programmers so they could access it themselves without notice, or just flaws that hadn't been detected. But the biggest point of vulnerability were user terminals, particularly government ones, but also many from within private businesses that were tied to the network. Even the military wasn't immune to bad user practices that left holes in the security of the network. Maya knew how easy it was to break in that way because she had done it herself. Her hobby after all was being a hacker.

While she would never tout her own abilities, she was an excellent technician and was second to only Dr. Akagi herself on the staff. Hacking was something she started in college due to boredom. She didn't go out much and wasn't in high demand for dates, spending most of her time studying. She began by just seeing what she could get into. Finding that she had a talent for it, she took to it in earnest, especially after another hacker had tried to break into her computer. At that point she started going after other hackers who were looking to steal or do damage with their activities. It was a thrill for her, she got to be a superhero of sorts by knocking down some pretty nasty and notorious hackers and putting an end to their schemes.

Dr. Akagi herself liked to hack as well and was the only other person to know of her hobby. But she went after more dangerous game, probing the other MAGI systems through a network of proxy servers that made her harder to track, or taking shots at high end military systems. She left trails that only she could find again to give her ways in to be used later. Between the two of them they should be able to find multiple avenues to let them into the systems the other MAGI's linked with.

Sadly government systems, no matter how good they claimed their security was, were pretty easy to get into. People would leave terminals on without logging out, or they used passwords that were ridiculously easy to crack. Security software and hardware didn't get upgraded as often as it should. All it took was one terminal that was compromised and you could work your way into every database in the government system, then easily branch out to others. She had found it ridiculously easy to get into the Finance Ministry's system, and then break into the network of the stock exchange and the banking network. Systems that should have been some of the most secure in any country.

The MAGI systems were linked to all of these so that they could monitor for fraudulent activity and track economic trends. They were also linked to things like the city public transit systems, the electrical grid and the power stations themselves. Getting into any of these other systems was the easy part, back hacking into the MAGI was the harder part but that particular job was going to be tackled by Dr. Akagi herself. After all, who knew more about how the MAGI worked than her?

She put pen to paper and began making a list of all of the other large subsystems that connected to the MAGI, a little electronic research and her own knowledge would help compile a more complete list that she could then start actively probing and making inroads to. The next question was how could they utilize those systems to pull resources away from the other MAGI's ability to attack them here. There was a possibility that Dr. Akagi could get into at least one and plant something in it's systems and have it share it with the others once the attack started, but that was the riskiest proposition and the one most likely to fail or be stopped. If the systems were being tied up it would have a better chance of success, but that still meant that the most important part of the plan was to find a way to tie up the system in the first place.

She turned the page, leaving her list of systems to probe for later and began thinking of ways to make them tie up the networks and the MAGI once they were compromised. The key was to make the MAGI process so much data that it had to divert resources. That would work until they blocked the links to those outside systems, so it would be important to make it so they either couldn't do that, or that if they tried it would trigger something else, sort of a cascade effect.

Since the MAGI held back up information for most of the important government departments, they could force it to do back ups of that information, maybe even multiple back ups. If they attempted to stop it, make it spawn more back ups. Make them run calculations for the national budget and projections through the banking and stock market systems. Flood the system with repeating error messages from the transit system and the power grid. Start diagnostic programs for every system they were connected to. Make the MAGI think there was a military attack underway and flood the system with false sensor images from everything from ground radar stations to satellite feeds. Absolutely anything they could think of that would make the enemy MAGI systems tie up resources was good, even if they could only confuse things long enough to potentially slip in a virus.

That would be the last piece of the project. When Dr. Akagi got back they could discuss that option. She would have a better idea of what was possible, what was most vulnerable to what kind of virus and what they might have the best chance of getting into the systems through their security. She had a pretty good idea that her mentor already had something in mind for that.

She finally felt like she had a chance to accomplish something now. All along, all she had done when they were being attacked by the Angels was monitor the Eva's and shake in fear at her station as she listened to the fear and the pain in the pilot's voices as they fought, Shinji's in particular. She knew that he was scared, but despite that he kept going out to fight and kept them all alive, she was very grateful to him for that and wished she had some way to express that gratitude. She didn't have that kind of bravery but she still wished that there was something more that she could do. Now she could but it was a double edged sword. The price had been learning that things were far worse than she had known and that her Sempai was up to her neck in it. It tied her guts in knots but she couldn't sit and do nothing now. She might be scared, more scared than she was before but her conscience wouldn't let her do nothing.

* * *

Had to give Gendo a little bit of what he deserves.

Please leave a review if you would be so kind.

And while you're here, check out my other stories.


	18. Chapter 18

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

 **Transposed**

 _ **Chapter 18**_

 _ **Rei's Inner World**_

To say that Shinji was blown away by the truth of just exactly where it was he was standing would be an understatement of epic proportions. He was inside some part of another person's mind. Rei's mind. He had to admit that it was a rather peaceful scene. The motionless, tranquil body of water that seemingly stretched on forever, the reddish, star filled sky. Though he kind of wished that the water was just a little bit higher or that he wasn't here naked. He supposed that he should be used to that by now after having spent the last four days that way inside of Unit-01's core world. It was difficult for him to admit, but he had actually been getting used to it. Somehow the nakedness of his soul form felt quite a lot different that being naked in his physical body. Little wonder his Mom now found clothing to be restrictive and uncomfortable after ten years of that.

The last four days spent in the core with Misato and Shogoki had done a lot to help him recover from the last Angel's attack. He was able to rest and the three of them talked a lot about all kinds of things. He and Misato both still felt some of the effects of the attack but they had started to become more comfortable with each other given what they had seen from each others memories. Maybe even becoming more comfortable with each other than they had been even before that. He had also become more comfortable around Shogoki which she seemed to be quite happy about.

He was pretty sure that she was more than just the Eva's consciousness and he had an idea about that. With what his mother had told him about the Eva itself and how it was constructed, along with some clues that Shogoki herself had dropped, he was sure he knew who and what she was. Surprisingly he wasn't totally freaked out by that if he was actually right. Then again his freak out capacity was pretty much maxed out right now and didn't have room for anything else. He would ask his mother about it when he had the chance.

The three of them had actually managed to have a little fun too over the last couple of days. Once they had begun to recover and feel a little better, Misato's fun loving and teasing nature had begun to resurface again. There was some joking and teasing, a few chases up and down the beach and around the small cottage, and they even managed to convince him to let them teach him how to swim. That was where a lot of the teasing took place since being naked and in such close contact with them caused a certain part of the male anatomy known to have a mind of its own to act accordingly despite his wishes to the contrary. He just hoped that it behaved itself here since standing naked in front of an equally naked Rei was going to be tough enough without that problem cropping up.

They had told him not to worry about it, either in their presence or here, since it was a very normal reaction and especially for a boy in his teens. They certainly weren't offended and they doubted that Rei would be either but that didn't exactly ease his mind. Considering how bothersome that particular part of his anatomy had been, he was pretty sure they had been trying to make him react as much as possible. Well, to be honest, if any part of their antics had been to get him so that he wasn't so embarrassed by his reactions to them, it had worked to some degree. He had become at least a little less mortified by getting aroused in their presence. He actually had little choice really because it wasn't like the situation had been going to change anytime soon.

Secretly, he had loved all of the attention they had showed him now matter how or what it entailed, even with the embarrassment, and somehow he could tell that it had all been genuine. He had felt something from them that he had been missing for nearly his entire life. They cared about him. They loved him and they wanted him to be happy and enjoy his life and they wanted to be part of it. They had even managed to convince him, or very nearly at least, that it was alright for him to have feelings for more than just one person. It was alright for him to have strong feelings for Misato and for Rei and even have growing feelings for Shogoki herself.

He wondered if maybe it was because he had been so lonely for so long with no one to share his own feelings or even any happy experiences with and he was overcompensating. They told him that even if he was, it didn't matter. He was entitled to being loved and cared for as much or more than anyone else and if his feelings encompassed more than just one person, so what? It was something that was worth exploring and if he was fortunate enough to have his affections returned by those he was interested in, take it and run with it. So long as he was happy that was all that should really matter. Anyone who didn't like that could just go and mind their own business. Of course leave it to Misato to suggest that since he was a world saving hero he deserved to have his own harem. He very nearly fainted at the suggestion.

A shimmer in the air and a ripple in the water marked the arrival of Rei and Shogoki. He had to struggle to keep from showing his shock at Ayanami's appearance. Shogoki had told him what she had tried to do, how she had struggled so hard to try and come to his aid when the Angel had him pinned in its attack. She had explained how in this place where she retreated to find some peace and calm, her body might show the damage it had taken in the physical world if she was sufficiently upset or afflicted by a depressed and despairing mood.

Shogoki had also told him how much damage she had done to herself and how upset she was that she had failed in her attempt to help him, and that her temperamental Eva wouldn't even start up for her to try and do so. He could see that damage on her now and he could tell the difference between what was new and what she had sustained from being beaten by Asuka. She also looked scared and nervous, something he had never seen from her before.

"See little one," Shogoki gently spoke to her. "As I said, Shinji is uninjured and is doing well."

There was a slight look of relief in her eyes as she raised them to look at him, but they were soon downcast again. "Ikari. I...I am sorry that I was unable to come to your aid."

Despite the conclusions she had come to the last time she was here and the burgeoning sense of resolve that she had discovered, she found herself in the same situation she had been in then. She was so unsure of herself and her place and so afraid for what Shinji thought of her that she could barely function and it had caused her to bring all of her wounds with her again to this place of respite.

He swallowed and tried to quell his own nervousness. "Ayanami..." He took a deep breath and bowed deeply to her. "Thank you. You wanted to come and help and you tried so hard...I'm grateful. I'm sorry that you got hurt so much."

She was shocked at his words and even more so by his bow. She did not feel that she deserved such gestures from him when she had been unable to do anything. "Ikari..."

"Y-you can just call me Shinji if you want," he told her quietly as he straightened.

First thanking her, then encouraging her to be more familiar...she didn't understand. She had failed him. Shouldn't he be disappointed or angry that he had to face the Angel alone?

When she didn't say anything he wasn't sure what to think, but there was something else he needed to say to her. "I'm sorry Ayanami," he began, stunning her yet again. "When I came to visit you...I know now that you knew I was there. I said something stupid and I ran like a coward." He was on the verge of tears. "I'm so sorry Ayanami...what you are doesn't matter! I don't care. You're Ayanami and you're my friend." He bowed again. "Please forgive me."

"Ikari...Shinji..." she didn't even notice the tears that had begun to fall from her eyes. He did not care what she was or how she came to be. She sensed no dishonesty in his words and for the first time since Unit 01 released both him and his mother, maybe for the first time ever, she felt a small sense of what she supposed was hope. "I wish to still be your friend as well," she responded quietly. She really had no idea what to say or if what she had said was adequate, but it was the truth. She really did wish to remain as his friend. She realized that to not be was something she did not want to even think about.

"Thank you Ayanami," Shinji said, greatly relieved.

"Rei," she said, finally able to look him in the eye with some level of confidence. "If I am to use your name then you may use mine."

"Alright. Rei," he said smiling. It felt nice to say her name and to her it somehow felt nice to hear him say it.

"I'm proud of you both," Shogoki said, smiling herself. "I told you things would work out just fine."

"Rei," he said in astonishment. "Your wounds...they're fading away."

"That's because her mind is much more at ease now," Shogoki explained. "You are well and you accept who and what she is and you wish to still be friends. You too seem more at ease now Shinji."

"I'd be more at ease if I wasn't naked," he muttered. It was taking some effort not to react to Rei's nakedness, especially now that the spectre of her wounds had disappeared from her body, leaving behind nothing but unblemished, smooth, pale skin.

Shogoki laughed lightly. "Well it's only fair Shinji. If you get to see her naked, she should get to see you naked too. This is similar to the core world and you know how that works. Besides, you got to see her naked once before right? This makes things even."

He turned red at the memory of that visit to her apartment and his accidental squeezing of her breast. Damn, why did Shogoki have to remind him of that? He felt himself begin to react to that guiltily held memory.

"I..." Rei began. For some reason her cheeks began to feel warm and her eyes kept straying toward Shinji's current dilemma. "I have seen Shinji naked before."

"What?" he squeaked.

"Oh, the naked sync test before the Eleventh Angel, "Shogoki realized. "You peeked didn't you?"

Rei nodded slightly. She had been curious. Soryu had been throwing a tantrum about it, for some reason it was a problem for her to be seen naked and apparently by Shinji in particular. She had no qualms herself about being naked but the Second Child's ranting had served to remind her that once again she was naked within Shinji's sight and it had reminded her of that day in her apartment and how she had felt then. So for once she allowed her curiosity to have its way and she looked.

"Can't blame you," Shogoki added. "He does have a cute butt."

She didn't know about that, she had never taken into consideration the level of beauty of anyone's particular body parts, and she did not know really what would constitute a butt being cute, but she was not displeased by what she saw that day. Or what she was seeing now and she couldn't explain why.

"I think you've been spending too much time around Misato," Shinji accused. "She's a bad influence on you."

"I like to think the time I have spent with her has been both fun and educational for the both of us," she countered. "Especially where you are concerned." She grinned. "Now, I'll leave the two of you alone for a bit and you can talk or...whatever." She disappeared before either of them could respond.

The silence quickly became awkward. Neither of them was exactly known for being talkative and normally they both found a certain amount of comfort in the quiet, but this wasn't one of those times. Added to it was the nervousness of two young people who liked each other.

Shinji found himself looking at the sky. "The stars look so close and there are so many. Do you...like looking at the stars?" he asked tentatively.

"Yes," she answered. "I also like the water. I find both to be comforting."

"That must be why your inner space looks like this then," he surmised. "It's hard to believe that this is a place that exists within another person's mind and that I'm in it. Thank you for allowing me to see it Rei."

She felt that warmth on her cheeks again. "Shogoki felt that it may be best for us to meet here rather than wait until I awakened. I would never have allowed anyone else to see this place."

"Do you come here a lot?" he asked.

"When I am hurt or when I am confused or troubled." She sank down to her knees so that just her head and shoulders were above the water. "After I was injured I have been here a great deal."

Realizing just where her new position left her eye level, he sunk down into the water as well. "Why didn't you fight back?" he asked, hoping he wasn't pushing his luck. He didn't want to offend her or make her angry.

She leaned back and let herself float atop the water, uncaring that she was displaying herself to him. "I had nothing left. With the return of Yui Ikari the purpose for which I had been created was gone and the Commander did not issue me any further orders. I had no direction."

"Did you want to die?"

"Life...has been painful," she continued. "I have been injured by the Eva many times and downloading my memory and experiences for the Dummy Plug system is exhausting. I have been alone with just a single purpose for my existence and everything else in life was deemed irrelevant. I was not even unique but one of many and I could easily be replaced by another. The culmination of my purpose was to be my reward and my release from the harshness and pain of life. I looked forward to it...until something began to confuse that desire."

"What was that?" he asked.

She turned her head toward him. "You. You became important to me when nothing but my given purpose ever had been. Despite your fears you piloted in my stead to protect me even though you did not know me. I was confused by this until I got to know you and saw that it was your nature despite your own misgivings about yourself. Even though my response has been lacking, you showed me what it felt like to have a friend. I realized that I did not want to lose that but I did not know how to keep it. I was afraid."

"What were you afraid of?" he felt himself choking up a little. He knew from what he had been told that life had not been easy for her, how little of a life she had actually been allowed and how she had been conditioned to see everything not relating to her purpose as irrelevant. She had even been forced to live in what was essentially a condemned building just so she could be isolated even further. But to hear her telling it, even with the usual lack of emotion in her voice or maybe because of it, it was all just so sad.

"Of everything," she said, looking back up at the stars. "Of no longer having a purpose. Fearing that at any moment I could be taken into the depths of the base and disposed of. I felt lost and alone and did not know what to do. After you came out of the Eva I waited in the hospital but I was not allowed to see you and I feared that I never would again. I feared that you would find out what I was. I cried. I had never cried before or felt such inner pain. I did not know what else to do."

"Sometimes that's all we can do Rei," he offered.

"I cried a great deal," she continued. "After you and your mother had awakened I sought to speak with her but I could not go through with it. I was afraid that she would be disgusted by what I was and how I was created. Soryu found me in the stairwell. She was not herself, she seemed to be arguing with herself like there were two of her. I gave up. I offered no resistance and allowed her to do as she wished. I simply wanted the pain I was feeling to stop. I was no longer needed and did not know what to do."

"I needed you to still be my friend Rei," he said tearfully. "It would hurt so much to lose you. I shouldn't have went to see you that night. It was too soon after learning about everything and I messed up and hurt you more and I'm so sorry."

 _'It would hurt so much to lose you'._ A warm feeling flooded her being. "You truly do not care what I am?" He had said before that he didn't, but she needed to hear it again. She needed to have that to hang onto.

He wiped the tears from his eyes and shook his head. A smile came to his lips. "You're Rei Ayanami, that's all that matters to me." For the second time, her got to see her smile. He already thought that she was pretty but she was even more so when she smiled, genuinely smiled like she was right now.

"Then I am happy," she said. "I am afraid however that I will need help learning how to live rather than to simply exist."

He rubbed the back of his head nervously. "I think we're kind of the same that way," he said. "I haven't been doing a lot more than just existing either. But we can figure it out together and I think we'll have a little help."

"Your mother?" she asked. It was clear that she was still unclear where she stood in the eyes of Yui Ikari.

He nodded. "She really wants to get to know you Rei and she wants to help. Any anger she has about you is directed at my father for creating you just so he could use you."

"She held me after I failed to come to your aid," she said. "I was despondent. Just as I lost consciousness I heard her thanking me for trying to help you."

"She wants to give us both a better life after the Angels are defeated," he told her. "One where we won't have to fight anymore or be used by people like my father. A life where we can just be normal and do normal things."

"It may be difficult at first but I wish to live that new life," she admitted. They remained silent for a few moments before she turned her head to him again and spoke. "Would you...float here with me for a while before you go back?"

He smiled. "Sure."

Before Shogoki and Misato taught him to swim, he wasn't much for the water. Thanks to them he was quickly losing that fear so he gladly let himself float next to Rei and enjoy the serenity of the water and the stars of her inner mindscape. They were happy to be there in each others company and neither of them really took notice when their hands drifted together. Neither of them tried to move away either.

* * *

 _ **The Eva Cages**_

Finally clad in some clothes of her own, a simple dark skirt and white blouse under her lab coat that she acquired from one of the few remaining open stores in the city, Yui stood looking at the silent behemoth before her. Not the purple one where her son currently was within the core, but the red one that contained at least a part of the soul of someone she had considered a friend. She had no concerns about her son's well being, she had been getting regular updates and replays from Lilith. She supposed as his mother she should be concerned about some of the teasing and innuendo that had taken place, but she had seen the positive affect it had on him. It had helped both he and Misato to start to recover from their ordeal during the last attack. It had been four days since then and even though he was in good hands, she couldn't wait to get him back.

At this moment however her concern was focused on Unit 02. From what she had determined through data records and by talking to Ritsuko and Professor Fuyutsuki, Asuka had never had the same level of contact with the soul within the Eva as Shinji had had with her. Not even close. With what was possibly coming according to what she had learned from Fuyutsuki, that needed to change. Besides the threat of a military attack there was the distinct possibility of attack by the mass production Eva units SEELE was building. The problem was that even with the intelligence Gendo had been able to gather against the old men, he hadn't been able to get a clear picture of how far along the construction of the MP units was.

One Eva could hold off and annihilate any army, several armies, all by itself with little effort. But against what could be as many as nine mass production Evangelions controlled by a dummy plug system they would need all three units operating. All of them were ready for battle but Shinji was currently the only pilot available, or at least he would be when he emerged from the core sometime today. Rei should be at least minimally able within a few days, Ritsuko had been cutting back the medication that kept Rei's S2 organ largely dormant so her healing should now speed up. The remaining question was Asuka.

Fuyutsuki had talked to her doctors and they said that she appeared to be stable and had been talking to them quite freely. It seemed that the trauma surrounding her mother's death had caused a split of sorts to begin in her personality. It wasn't until she came to Tokyo 3 that the two separated parts began to interact and the situation became worse at every perceived failure or slight. It seemed that what had been the dominant and aggressive side was no longer present but it was too soon for them to determine if it had just gone dormant or if as Asuka had described it, it had shattered and burned away to nothing after the incident with Rei.

The aspect they were seeing of her now was the scared girl who had lost her mother and who was overflowing with remorse for they way she had treated others for so long, and for what she had done to Rei. She had wanted to stop it but the control her other half exerted had been too strong until the deed had already been done. She was filled with guilt for not being there when she was needed during the last attack and for weakening their overall strength.

One of the crucial points for the girl had been in discovering that a part of her mother's soul resided within Unit 02 and if there was ever any hope of her being able to get back in the pilot's chair, it rested in getting Kyoko Soryu to reach out and make meaningful contact with her daughter. At least enough contact for the girl to know that she really was there. She had read the reports of Kyoko's behaviour after the failed sync test that tore her soul in half, how she treated a doll like it was her daughter yet didn't seem to recognize her own flesh and blood child, calling her 'that mean little girl.' By all accounts Asuka had loved her mother very much and that must have been a devastating thing for her even if she didn't show it.

She didn't like the idea of trying to make the girl pilot again. If she had her way none of them would ever have to do it again but circumstances were stacked up against them and there may be no other choice. She was the most highly trained of the pilots and was the most proficient of them with any weapon or with none. It disgusted her that Gendo's role for the girl was to essentially be cannon fodder to keep Rei and Shinji alive so he could use them as he intended, he really hadn't cared what would happen to her otherwise. Another victim of his grand scenario and yet another that her initial support of the Instrumentality Project had helped bring to ruin.

"Were you afraid to let her know that you were there Kyoko?" she asked the red behemoth. She knew it was listening, had known that it was watching her since she arrived in the cages. "Did you try or did she shut you out from the start in her drive to prove herself? When you saw how stubborn and aggressive and mean she was becoming, did you blame yourself and hide from her?"

In a way, mother and daughter had very similar things happen to them. When the Eva took part of Kyoko's soul, it was the darker side of her that was left behind in her body. Witnessing her insanity and finding her hanging from the ceiling had a similar effect on Asuka, burying the kinder, gentler side of her and letting the darker side have free reign to steer the ship. Seemingly now both of their dark sides were gone.

"She needs to know Kyoko," she continued. "For better or worse and damn us all to hell for it, she will have to get back in the seat. But for it to work and for her to survive she will need to know that you are there, that you have always been there with her. She's a scared and hurt little girl that needs her mother just like my Shinji needed his. We were both fools for what we did and our children have had to pay too high of a price for it. She sat here in this very spot talking to you, begging for some sign that you were there. You can't be afraid anymore to show her that you are Kyoko."

She heard the clacking of heels and turned to see Ritsuko approaching her, a cup of coffee in each hand. She looked less bedraggled than she had been. It seemed that stepping out of the dark side and back into the light had been good for her. So had spending her time working closely with Maya.

"Think she heard you?" Ritsuko asked as she handed her a cup. Yui raised a brow at the gesture. "It's the good stuff, not that toxic waste from the command deck."

"Thank you my caffeinated angel," she joked before taking a sip. She had been keeping some long hours herself and was grateful for the jolt this would provide. "She heard me. The question is if she will do anything."

"The other big question concerns Asuka herself," Ritsuko said. "If she is even able to be put back in the plug, will she do it now?"

"I suspect that she will given the guilt she seems to be feeling over not piloting, " Yui answered. "But it might come down to there being no choice either way even if she can't or won't just to keep her safe from a potential invasion of the base. Taking out the pilots would keep our Eva's from opposing them. They know they can't stand against them otherwise."

"I wish we could do something about the mass production units," Ritsuko mused. "But thus far I haven't been able to find a usable computer link into the facilities building them. I have a couple of possibilities to try yet."

"What about your hacking project?" Yui asked.

"We have several avenues into outside systems connected to the other MAGI and writing the routines to overtake them and do what we want with them are easy enough to do," Ritsuko explained. "Maya has a lot of that done already. We've been probing the other MAGI to see how they react and I think I may have found a possible backdoor to them thanks to a clue in my Mother's notes. The other systems were essentially copied off of this one and while their techs are good they don't have the advantage of the developer and inventor's knowledge. Or the routines and bugs she hid in the subsystems so that she had a way in if she wanted it. I seriously doubt they have found any of them. I'll be looking into it more later today."

"I wish you luck then," Yui responded. "Being able to turn the tables on them when the time comes will be invaluable."

"Can we really stop what SEELE is doing?" Ritsuko asked. She had been in too deep and knew too much of what was going and she knew what kind of odds they faced.

"We can and we will," Yui answered confidently. "We are putting things into place that they won't expect and we have an Angel on our side. And information from the sources Gendo put in place suggest that there are problems with the Committee right now. There hasn't even been any contact from them since the last attack."

"That does go against their usual procedure," Ritsuko mused. "Hopefully that is good news for us." She paused. "You went and saw Gendo yesterday didn't you?"

Yui sighed. "I did. He seems a little broken now. I think the full gravity of what he has done and what it cost him has finally hit him full bore. It almost makes me regret what we did but then I remember what he has done to his own son and everyone else around him and that sympathy leaves me. I never would have been or felt this vindictive before, this is not how I was ten years ago. I think I was influenced a bit by Unit 01's bestial nature before Lilith began to regain herself, and probably by my own guilt and regrets as well. He's a convenient target."

"And a deserving one," Ritsuko said. "I know that sounds very cruel of me but I can't help it. I know I am at least as equally guilty for my own situation as he is, I was naive and allowed him to pull me into his madness but I can't help but enjoy his misery."

"Understandable," Yui responded. Far be it from her to try and tell anyone they weren't entitled to their grief and anger...or their revenge for the things Gendo had done to them. "We certainly are a messed up bunch around here, aren't we."

"We most definitely are," Ritsuko agreed.

Yui bumped her coffee cup against hers. "To the inmates taking over the asylum."

"Here, here," Ritsuko agreed, grinning.

Yui went to speak again then paused. "Ah, it seems Shinji is about to return."

"Okay, that freaks me out," Ritsuko said. "I still can't believe that you can telepathically talk to Lilith."

Yui smiled. "It freaked me out a little at first too, but it's second nature now. I see and find out some interesting things too."

Ritsuko just shook her head. "Let's go welcome back your son. The sooner I give him the once over, the sooner you can take him home."

Yui took one last look up at Unit 2 as they began walking. She smirked when she saw a faint glow coming from the Eva's four eyes.

* * *

AN: Depending upon which form of media you look at, you get a different view of Kyoko Soryu. In the anime, we don't learn much about her. In the manga, she was an unstable hack who tried to poison Asuka to get back at her ex-husband. (And this was before her soul got split in the contact experiment) In at least one of the spin off manga she is kind of a ditsy goof. I figure that in order for her to be cooperative with Asuka within the Eva, having her be a nut job wouldn't work well. I may not do much with her but she certainly won't be the version that tried to poison her own daughter.

Please leave a review if you would be so kind.

And while you're here, check out my other stories.


	19. Chapter 19

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

 **Transposed**

 _ **Chapter 19**_

The morning commute was something that Kouzou Fuyutsuki often took a small level of pleasure in. The commuter train trip from the station near his apartment, to and down into the Geo-front gave him enough time to enjoy a cup of coffee and a look at the paper, be it in print or electronically on his tablet. The city paper was still going despite the number of people who had left the city though more of its content these days was world news they were getting from the major wire services. All in all it was a last moment of peace before the dark chaos of NERV's Tokyo 3 facility had him in its grip again for another day.

It was a routine he rather enjoyed and because of its routine nature he had stopped being as vigilant as he once was. Maybe it was because the daily grind of lies and dark conspiracies had tired him and dulled his instincts, or maybe he was just feeling too tired and old to care anymore. Perhaps he put too much faith in Section 2 to actually be doing their jobs when he should know better than that by now. Often their job performance was lacklustre at best and often downright incompetent. That was why he didn't notice that things were not as they often otherwise were this morning until someone sat down across from him and he realized the train car was rather silent.

Besides the man across from him there were six others in the car. A man and a woman stood by the doors at either end of the car, and two men stood by the middle doors. They were all either Caucasian or Asian and were all dressed casually, but to his accustomed eye they all had the bearing of highly trained military people. As did the man sitting across from him. He was dressed in a simple dark business suit with a white shirt and dark striped tie. He was Caucasian and sporting neatly trimmed hair and a beard, both liberally sprinkled with grey. He was solidly built with the same military bearing as the others but with much more of an aura of authority around him.

"No need to be worried Sub-Commander Fuyutsuki," the man spoke, his deep voice carrying a slight, faded hint of Scotland to it. "We are not here to cause you any harm."

He sighed and folded his newspaper. "Glad to know, especially since it seems I wasn't paying enough attention to my surroundings."

The man shrugged. "I would imagine you have more than enough other things on your mind already. It's fortunate that you ran into us though, there were some fellows from SEELE waiting for you but we persuaded them that it was a bad idea. Apparently the Committee, or just Kiel in particular wished to ask you some questions about what has been going on and about the last Angel attack."

"Just who are you?" Fuyutsuki asked.

"Excuse my bad manners for not introducing myself," the man said with a polite smile. "Colonel William McKinnley, United Nations Investigations Office, Special Investigation Service."

Fuyutsuki's eyes widened. He was certainly aware of the existence of the UN's Investigations Office, and through Gendo's intelligence gathering he knew of the SIS but didn't know much about them. No one did except that it was generally acknowledged as a bad idea to have them looking for you. They were the bogeymen of the Intelligence and criminal worlds, an entity that some dismissed as being a fairy tale made up by nervous types that jumped at shadows.

"Well that explains why you know about SEELE," he said, trying to remain calm. "What do you want with my old bones?"

"We've known about SEELE's existence for a long time. Up until recently we thought they were a group that in the aftermath of Second Impact was trying to gain control and govern the world from the shadows. Sadly we haven't been able to do very much about them except nibble around the edges," the Colonel said, obviously not happy about that truth. "However, we came into some information lately that has changed that and you can imagine our shock when we learned what they were really up to. The man who brought us that info said that the best person to try and make contact with that had a position of power while possibly still retaining a conscience was you."

"To my eternal regret I didn't listen to that conscience nearly enough," Fuyutsuki said. "So who was it that recommended me so highly?"

"Ryouji Kaji," McKinnley answered. "It seems that when Yui Ikari emerged from Unit 01 Gendo Ikari had a moment of humanity strike him and he gave Kaji all of the information on his and SEELE's plans and turned him loose to find someone to give it to. He found us."

"That bastard," Fuyutsuki swore. "He never said a word about it."

"According to Kaji his reasons were to hedge against the possibility that he would continue on with his own plans regardless of his wife's return."

"We were afraid of the same thing so we recently began taking steps to limit his options," Fuyutsuki said. "I assume then that you are aware that he possessed a fragment of the First Angel, Adam?" The man nodded. "We removed it from his possession and destroyed it a few days ago and we've essentially put him on a leash," Fuyutsuki explained. "He can't do anything that we won't know about."

"When you say we...?" McKinnley asked.

"Yui, Dr. Akagi, and myself," he answered. "We're going to do everything we can to make sure Third Impact doesn't happen."

"I'm glad to hear that and I believe that we recently removed a couple of obstacles for you," McKinnley said, seeming rather pleased.

"Oh, what would those be?" Fuyutsuki was intrigued.

"As you are no doubt aware the Tokyo-3 branch of NERV leaks info to SEELE like water through a sieve."

Fuyutsuki nodded. "Finding and plugging those leaks has been almost impossible although most of what gets out doesn't seem to bother Gendo greatly. He seems to enjoy the cat and mouse game he plays with SEELE."

"Your head of Section 2 seems to be the conduit for that outflow," the Colonel informed him. "We picked him up last night. Seems he has a weakness for booze and hookers so you can imagine how we reeled him in. He has several of his men as well as a number of the uniformed security troops in his pocket passing anything interesting they see on to him."

Fuyutsuki blanched. "Weeding them out is going to be hell on our security and protection, what little there already is of it."

The man nodded. "I've seen the plans and layout of the base and have a general feel for the level of training and competence of those people from speaking with Mr. Kaji. You are in deep shit there my friend but we can discuss that later. More interesting than your Section 2 head is who it was he was reporting to." He gestured to the newspaper on the seat next to Fuyutsuki. "You follow the news so I assume you are aware of the disappearance a couple of days ago of high profile businessman Daisuke Matsuzaka?"

Fuyutsuki nodded. "He's one of the most powerful figures in Japan not holding government office. As it is he wields a great deal of influence with a few government ministers."

"He happens to be the Japanese representative on the Instrumentality Committee," McKinnley continued. "And he controls the Minister of Home Affairs who currently has the most ability to influence the actions of the Prime Minister. Matsuzaka took over the spot vacated by the passing of Yui Ikari's grandfather. Your Section 2 man was answering to him and he passed the information on to Kiel and the rest of the Committee. We snatched him from the apartment belonging to his mistress. Even with the disarray within SEELE and the Committee since the assassination of Harold Connelly III and the wounds we've been able to finally inflict upon them since getting the information from Kaji, he still felt himself secure enough to go and enjoy his weekly tryst. And for such a powerful and supposedly tough man and hardcore SEELE true believer he wasn't that tough a nut to crack. All glory, no guts. Apparently martyrdom isn't his thing."

Fuyutsuki chuckled darkly. "The rest of the Committee must be soiling themselves right about now and Kiel must have his hands full trying to keep them together."

"The most panic prone were already jumping at shadows when they lost Connelly which created a few opportunities for us to take advantage of," he explained. "But Matsuzaka's disappearance already has a couple of them running for the hills. If we haven't rounded them up yet, we'll have them shortly. Dead or alive."

"You haven't been wasting any time have you?" Fuyutsuki asked.

"As I said before, we've been chasing after SEELE for years," McKinnley began. "We've had notions of who was doing certain things but never enough proof of it to warrant going after them. The information that was brought to us unlocked enough doors that we were able to start linking things together and considering what was at stake we were able to take the gloves off and start hitting them hard. Black Ops are so named for a reason and the potential end of humanity more than allows for a little extra judicial action."

Fuyutsuki sighed heavily. "And I have myself right up to my old neck in all of this because I was too afraid for my life to take a stand against it and became a willing participant. Which in the end would result in my death anyway. What a twisted notion."

"Mankind's survival instincts," McKinnley mused. "We do great or heinous things that we may normally never do otherwise even if it only gives us one more day out of the clutches of the Reaper. You said that you and your colleagues are determined to put the brakes on Instrumentality. I would like to know what you intend to do in that regard, if there are things that you plan to do that may force SEELE's hand. If there is I would like to make sure my people don't get blindsided and are able to plan accordingly. I believe I can also give you at least a partial solution for your security problem."

"For that I would be grateful," Fuyutsuki said with some obvious relief. "As for our plans that would probably be best explained with Yui and Dr. Akagi present. Yui isn't on base at the moment however, she's at home with her son but they are expected to come in later."

"I am aware," the Colonel told him. "You weren't the only one SEELE was looking to bring in today for a conversation." He raised a hand to stall any worries from the old professor. "Don't worry, my two best operatives are playing guardian angel. Dr. Ikari and her son will both be fine. The SEELE goons and their Section 2 helpers, not so much I suspect."

"I pray that it is so," Fuyutsuki sighed. "They've only just been reunited, I would hate to see anything happen to either one of them."

"You have my word," the Colonel promised. His tone was solemn, but the small smile that graced his lips was almost predatory. "They could not be in better hands."

* * *

 _ **Gendo's Private Geo Front Apartment**_

He sat at the desk in his home office, in his uniform except for the jacket, going over the base status reports of the last few days. Outwardly most observers would see no difference in his usual cold and commanding demeanour. Those few that knew him the most however would see the sag that had crept into his posture and in the menacing aura that surrounded him. He was a man whose selfish obsession had been broken by the very object of that obsession. He had thought he had hit bottom when he realized Yui was not about to forgive him shortly after her return. He had been wrong. The bottom came a few days ago in his office.

He had never been one to believe in abstract concepts like karma. To him, everything that came to you in your life was based upon your own choices and actions and the work you put in to attain it. Even in his younger days he had never thought of the ills of his life to be the product of karma. He knew it to be the product of bad relationships with those around him. He always believed that the way he had been treated by others was their responsibility and wasn't some form of divine punishment. As he grew older he became equally as responsible for his own treatment considering how he tended to antagonize those around him and get in frequent fights with them.

A psychiatrist would probably tell him that he became this way because he refused to take any responsibility for himself and blamed all of his ill behaviour on others who had wronged him and mistreated him during his upbringing. Instead of trying to change his own behaviour and become something better, he wallowed in his self pity and came to blame the world for everything and thus would just as soon see it all disappear.

There may be some merit in that he supposed, and those who believed in karma would say he was reaping what he had sown and was getting his just reward for it. Maybe they were right. He was not a good man, never had been and he had done so many things that would label him as possibly one of the worst ever in the history of mankind. Not that he actually cared. There had been a time once when maybe that could have been stopped and even reversed. Falling in love with Yui had been the best thing that had ever happened to him in his life. Being with her had made him the happiest that he had ever been. Yet he was still willing to end the world rather than learn to live in it with her.

Finding out about SEELE's Human Instrumentality Project had happened at the right moment to prevent him taking a different direction. If he had found out a year later, maybe only a few months later he may have taken a different path. Being with Yui had been changing him. He was seeing a better side of life in the arms of someone who had proven him wrong in his notion that no one could or would ever love him. But he was still teetering on the edge between that and the pains and insecurities of his past when he learned of the HIP and he fell into it headlong and enthusiastically.

He managed to pull her in with him and he was sure that if had decided to work against SEELE's plans she would have worked just as hard as she did for it. He also suspected that she still would have wound up inside Unit 01 anyway for Shinji's sake and he had little doubt that in that eventuality he would have then hijacked SEELE's scenario just like he had been doing anyway.

He supposed it did no good to wish that she had not allowed the Eva to take her. It seemed to be an inevitability no matter which way things went. He supposed that he resented Shinji for being the reason why she did it. He had always had a level of resentment that his birth had taken her attention from being solely on him and it only grew when she was gone. It made it so easy for him to do what he did to the boy when he began to enact his plans for Instrumentality.

He had miscalculated badly, or maybe he had just been supremely selfish to think that when Instrumentality occurred and he was reunited for that brief moment with her before all became nothing, that his last recollection and interaction with her would be one of love. He knew now that it would have been anger and hatred and that the fleeting moment of happiness he would have been expecting would have been shattered.

Being tasered by her and hearing the vitriol in her voice had been the last blow that broke him. She acted nothing like the kind and caring woman he had known and he knew at that instant that he was the reason why. He had done this to the woman he had loved so much that he was willing to become a monster, well an even bigger monster anyway, to be reunited with. He had turned what had once been love into hate and he deserved every bit of it that she could throw at him.

Now he and his plans were in tatters. His wavering and indecision after her emergence from the Eva had prompted her to act and take the choice out of his hands and by force at that. The fragment of Adam had been removed from him and destroyed. Rei's clones had been destroyed and by sometime later today so would the body of Lilith in Terminal Dogma. Her soul, her consciousness, repaired from the damage they had done to it now resided within Unit 01.

He sat back in his chair and regarded his heavily bandaged right hand. Now he was the puppet on the end of the strings held by someone else. Appearances needed to be maintained so he was still the Commander, but he was on a tight reign and would not be allowed to take any measure of independent action. As he was now he wasn't sure that he even wanted to. He was a defeated man and his plans had ultimately come to ruin by his own actions.

He knew there was no chance for redemption and he didn't want any. He had no use for such a thing and never had. Even if he had destroyed any feelings of love Yui ever had for him he still loved her. The very least that he could do was fill the role that she required of him now. It would never make up for what he had done, would never balance the scales of karma that some believed in, but it is was the only even remotely honourable thing he could still do. For ever taking a chance on him in the first place he owed her at least that much. The question was, after all this time and everything he had done, could he pay even that token amount. Could he abandon everything he had worked towards and go against it?

* * *

 _ **Outside The Ikari (Katsuragi) Apartment Building**_

"She said she didn't want to go with you."

The day had gotten off to a good start, Yui had thought. A good continuation from the day before. After Shinji returned from Unit 01's core and was given a clean bill of health by Dr. Akagi, they had walked home together. He was a little tired and she could tell he was a little ragged from the ordeal he had gone through but he wanted to enjoy the nice weather with her for a little while. It had surprised her, and maybe even him a little, when he began to talk about what had happened to him and Misato.

She was proud of him. He began talking without any prompting from her and didn't break down once. Sure, he was a little emotionally wobbly and she could tell it wasn't the easiest thing for him to talk about even after all the time he had spent talking to Lilith and Misato, but he got through it. He also told her about his visit with Rei and presented his theory to her about Shogoki. When she confirmed it and filled him in on the particulars about her she was even more impressed at how he took it. Formulating his theory had prepared him for the possibility of being right and his interactions with the Eva's resident soul had calmed any anxiety he had about her being the Second Angel. At least outwardly, she couldn't say what was going on inside of him.

After a late lunch and a nap he insisted on making dinner and she filled him in on what else had been going on while he was in the core. After dinner they just relaxed and watched a couple of movies that had survived Asuka's rampage. It was while watching them that she realized just how much of life and the world in general she had missed over the last ten years. It gave her a sense of disconnection and it was going to take a while to catch up.

In the morning she awoke to the aroma of breakfast cooking and was proud of herself that she had managed make it to the table without forgetting to get dressed this time. After showering and having a bit of a relaxing soak until it was time to go, they set out on foot for the base. The weather was nice once again today and walking was better than riding with the Section 2 people watching the apartment. There was something about them she didn't like and they really didn't seem like they were all that serious about their jobs. Like many of their comrades, they had the look of third rate mercenary goons. They made her wonder how much money Gendo had wasted in hiring them.

They hadn't gone far when two cars similar to the those used by Section 2 pulled up, one next to them and the other across the street. Two men sporting the typical dark suit and sunglasses look got out of the car nearest to them. She didn't recognize them as any of the Section 2 people she had been exposed to thus far and they certainly weren't part of the detail that had been assigned to her.

"Dr. Ikari, please come with us," the man closest to her spoke.

"Who are you?" she asked, suspecting that she already knew. "You aren't Section 2."

"The Chairman would like to speak with you," he said by way of answering.

 _'Interrogate, more likely,'_ she thought. "I have nothing to say to the Chairman and especially not when he sends his men to pull me off the street. We're not going with you."

"This isn't a request Dr. Ikari."

"She said she didn't want to go with you."

They all turned to see a very large man stepping out onto the sidewalk from the shadows of a privacy wall surrounding the property next to the apartment building. He was Caucasian and stood well over six feet tall and was thickly built. He was dressed casually in boots, jeans, and a dark shirt under a light windbreaker that was unzipped halfway. His green eyes seemed to take in everything around him even though his main focus was on the four people directly in front of him.

"This is none of your concern," the SEELE man told him coldly. His partner left his position by the front of the car and began making his way around. "Move along."

"I don't think I will," the stranger said evenly. "And I think two goons in bad suits trying to snatch a woman and her son off the street when they clearly don't want to go makes it very much my concern."

The SEELE thug coming around the car did exactly as he wanted him to, he stepped past Dr. Ikari and Shinji and right to him where he met him with a straight left jab that flattened his nose and sent him sprawling to the sidewalk. The first guy reached into his jacket, going for what he presumed to be a pistol holstered under his left arm. A high kick slammed into that hand, causing him to cry out as a couple of his fingers snapped, and sent the guy stumbling back against the car. The stranger stepped in and slammed him with a right. There was an audible crack as his jaw broke and a couple of teeth and a spray of blood flew out of his mouth. He slid down the side of the car to the ground, out cold before he landed.

An angry snarl told him the first guy was back in it, despite his watering eyes and profusely bleeding and very crooked nose. He threw a left handed punch but the stranger slipped it and rammed his knee into the SEELE thugs guts, doubling him over. He grabbed him by the scruff of the neck and rammed his head through the rear side window of the sedan. He left him hanging half in and half out of the car. Across the street the other two SEELE men where scrambling to get out of their car and draw their guns.

"Get down!" he warned the Ikari's as he pulled his own gun out from under the back of his windbreaker and aimed it over the roof of the car.

At the same time, further up the street where the Section 2 car was parked the two occupants were leaning over the fenders and looking under the opened hood, feigning car trouble as if that would absolve them of any blame for not following their charges and keeping Kiel's men from taking them. A tall woman with her long dark hair hanging in a braid behind her and dressed similarly to the man up the street watched them from the walled yard of the house they were parked in front of.

When her partner confronted the two SEELE goons down the street, she stepped out and quietly walked up to the car. The weren't paying any attention to anything behind them so it was almost too easy to get to them and take out the first guy. She simply walked up behind him and kicked him in the balls as he was leaned over the fender. As he shrieked in surprise and pain and crumpled to the sidewalk clutching his wounded manhood, she was already coming around the front of the car.

The hood was held up on a prop and a quick snap kick dislodged it and caused it to come down on the other guy as he was trying to stand upright and see what was going on. Before he could get himself out from under it she was there and kicked him hard in the knee, taking out his footing. With the hood still keeping him trapped she slammed a hard punch into his kidneys before finally lifting the hood with her left hand and grabbing him by the hair with her right. She slammed his head into the A-frame post between the door and the windshield, knocking him out. She disarmed him and unloaded his pistol before tossing it in the car and throwing the clip into the yard she had been watching them from. Going back around the car she finished the other guy off with a kick to the head. A small mercy for his aching balls. She disarmed him as well.

Looking up the street she saw the occupants of the second SEELE car scrambling out and focusing on her partner. Pulling her own pistol out from under her windbreaker she fired two quick shots while calmly walking forward, nailing the driver in the side and taking him down. Another double tap to the head took him out permanently. Her partner took down the other guy in a similar fashion and kept his weapon trained on the downed men as she advanced, kicked away their weapons, and checked to make sure they were no longer a threat.

She trusted him to have her covered just as he had trusted her to take down the two Section 2 operatives while he handled his targets and be done in time to turn her attention to the other SEELE goons and help cover his position. They had been teamed up for a few years now and they worked well together, both having implicit trust in the other.

"Clear!" she called out as she fished a wireless earpiece and microphone out of the pocket of her jacket and plugged it into her right ear.

"Clear!" he called back from his position. He put his own earpiece in just in time to hear his partner calling for their ride and the clean up crew and giving them instructions. "Are you two alright?" he asked as he continued to scan their surroundings. He didn't fail to notice that even though he had remained silent, Shinji had taken a protective position around his mother.

"We're fine," Yui answered. "But who are you?"

"I'm afraid introductions will have to wait Dr. Ikari until we are safely on our way to NERV."

A moment later a dark blue, full sized SUV, a red sedan, and two white vans came roaring down the street. The SUV pulled up between the two SEELE cars with the sedan behind it. One van stopped by the Section 2 car while the other pulled up behind the first SEELE car. He quickly ushered his charges into the back of the SUV, climbing in after them while his partner got in the other side. It was a bit cramped but tolerable. Before the doors were even shut the SUV took off, followed by the sedan. Yui was amused by the red faced look on her son as he was squashed up against the decidedly pretty woman next to him, while she wasn't upset in the least by the feel of the large, very solid man she was squeezed up against.

 _'Pervert'_ , Lilith sang in her head.

 _'Hush you'_ , Yui admonished good naturedly.

The woman turned and looked out the back window, mashing her assets into Shinji's arm and chest. "No signs of pursuit." She turned to the driver. "See any other potential hostiles around while you were coming in?"

"Nothing," the driver reported in a distinctive Australian accent. "Not even any other Section 2 cars in the neighbourhood."

"Team 3 reported that the other Section 2 car that was supposed to be out here was seen at a convenience store several blocks away," the man riding shotgun said. He was Japanese and looked more like he should be a salary man than a soldier.

"Either incompetent like most of them or on SEELE's payroll like the other two back there," the woman said.

"Got a message just before we picked you up," he continued. "The Colonel and his team have successfully picked up Sub-Commander Fuyutsuki and they'll be waiting for us at NERV."

"SEELE was after the Professor too?" Yui asked. "Kiel is starting to look desperate."

"We're making life miserable for him," the woman said. "And hopefully soon we will put an end to him and SEELE."

"So who is 'we'?" Yui asked.

The woman looked at her partner with a smirk. "You're so rude, you didn't even introduce yourself to them." He just rolled his eyes. "We're with the United Nations Investigations Office, Special Investigation Service. I'm Captain Melissa Lake and the big bear taking up all the space is Captain Matthew Riker." She gestured to the front. "The driver is Lenny and Gen is riding shotgun." Both men held up a hand in greeting.

"Never mind the ranks," Riker said dismissively. "They're just a bureaucratic thing to fill in some pencil pusher's organizational charts at UN Military HQ."

Lake smiled knowingly. "You're just pissed because no one calls you Sergeant Major anymore."

He snorted. "An officers rank makes it sound like I sit in an office all day drinking coffee and shuffling papers, never getting my hands dirty. It offends my sensibilities. Besides, I _earned_ that rank of Sergeant Major."

"You guys have been arguing about the pros and cons of being an officer all morning," Gen said, the amusement clear in his voice.

"Oy, you're going to get him all moody Mel," Lenny cracked.

"I _do not_ get moody," Riker countered. "And mind your driving or else I'll tie you in a knot."

If she hadn't seen them in action Yui would have been a bit incredulous at their banter and think they were something less than serious about their work. "Well, obviously you know who we are," she began. "And can I surmise that you have at least some idea of what SEELE is doing?"

"We know exactly what they and Commander Ikari have been planning," Riker answered. "A week ago a man named Ryouji Kaji brought us the entire scenario. The information was given to him by the Commander himself to be a fail safe against him going ahead with it anyway even though you had returned. He's not a terribly good spy but at least he picked the right people to give the information to."

"Kaji is a spy?" Shinji asked, rather surprised.

"He works for the Japanese military spying on NERV and SEELE in the role of a triple agent," Lake told him. "He spies on NERV for SEELE, and on SEELE for NERV. They probably both know about it but he hasn't turned up a lot that has been useful for his real employers or that would prompt either of them to take him out. He didn't even trust his real employer enough to give them what he gave us."

Shinji was conflicted. He kind of liked Kaji. With him being a spy, did that mean that his friendly overtures and his attempts to get back with Misato were all so that he could dig for information? Was there anything genuine about him or had he just been using everyone he interacted with? It had already been hard enough to swallow the information that he had brought the fragment of the First Angel to his father. Actually, he really hadn't had a lot of time to think about that. He had been told so much in such a short period of time and so much had been going on that some things had slipped into the background. Why would Kaji do that? Was it just to prove himself to his father? Had father used him like he did everyone else?

"So Gendo doesn't even trust himself," Yui said tightly. "That might be the smartest thing he's done in the last ten years. And it's a good thing he did."

"He was still going to go through with it?" Lake asked.

"He was unsure, but he had done nothing else to prevent it either," Yui answered. "Like always he was keeping all of his options on the table."

"With the information Kaji brought us we were finally able to start ripping into SEELE and have made progress," Lake said. "But I don't know if we've been able to put enough of a dent in them yet to even slow them down."

"We've already started taking Gendo's options away," Yui told her. "Myself, Fuyutsuki, and Dr. Akagi staged a bit of a palace coup and destroyed one of his needed components. For the most part what he needs to make Instrumentality happen are the same things SEELE needs. We were on our way to NERV to deprive him of another when all of this happened. I was stupid enough once to side with the Instrumentality Project." She gave Shinji's hand, which she had been holding in her lap since they got in the vehicle, a gentle squeeze. "I'm not about to let it go on now that I've come to my senses and can be with my son again."

"Sounds like our chances of ending this thing just got a lot better," Riker mused. "We've been hitting SEELE hard the last few days and we're snapping at their heels, but taking them down isn't enough if the means are still in place for Instrumentality."

"Sadly there are multiple ways that it can be done," Yui told them. "But before they are even able to try we will have reduced those ways and made preventing the rest far more manageable. You said your commanding officer was at NERV with Professor Fuyutsuki?"

"That's right," Lake confirmed.

"Then I assume he would like to meet with us and discuss how we can work together and stop this?"

She nodded. "That's the plan."

"Then I hope you're prepared to hear another revelation or two than what you already have," Yui warned. "Things that even Gendo didn't know and at least one that Kiel isn't even aware of."

Lake groaned. "Great, more things to give me nightmares."

* * *

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	20. Chapter 20

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

 **Transposed**

 _ **Chapter 20**_

The Psychiatric Evaluation Ward. It was NERV's way of dealing with personnel whose minds had broken but knew information that was deemed not for the eyes and ears of the general public. Even an honest and caring outside psychiatrist may feel compelled to break their oath of confidentiality if they learned of the certain inner workings of NERV. Secrets were to be kept even if it meant housing the ill at the base hospital facility. Making them disappear might be cleaner for the organization but it would prompt too many unwelcome questions to be asked. Better to make it look like compassion was in place even if it wasn't. The doctors and their intentions were genuine, Gendo Ikari's, not so much.

Like much of the rest of the hospital that Shinji had come to know far too well it was very quiet here, which to him right now was both good and bad. Good, because it was peaceful, bad because it gave him too much time to think without something to distract him. Upon arrival at the base and meeting the man in charge of the SIS, they had gone to one of the conference rooms to have a meeting. He didn't need to be there so he gathered his resolve and decided it was time he came to visit Asuka now that she could actually have visitors, at least on a restricted level.

The Sub Commander had contacted the head of the Psychiatric Department, the same doctor who was personally looking after Asuka, and made the arrangements. Dr. Tokita had been of the opinion that Asuka was stable enough to have a visitor and that it might do her some good. What Shinji hadn't been prepared for was the lengthy interview he underwent with Dr. Tokita before being shown to a lounge area that overlooked the grounds of the Geo-front.

The first thing the doctor wanted to know was how much he knew about Asuka's past. Admittedly, he didn't know much but he did know how she had lost her mother. The doctor then gave him a brief and simplified explanation of Asuka' condition. Though as one would expect he didn't go into any specific details or tell him anything that Asuka had said. The doctor then began to ask him a number of questions about Asuka. What had she had been like at home, at the base, at school? Her general behaviour and attitudes. He didn't like the idea of talking about her like that but the doctor said the information was important for him to get a better understanding of her and he needed him to be completely honest and not leave out any details no matter how unimportant he thought they might be.

Odd how it hadn't dawned on him before just how alike they were. They both lost their mothers to the Evangelion but Asuka pushed her pain inside and rarely visited it, showing the world a brash and challenging personality to hide that pain and push herself in an effort to get away from it, even if that meant trampling others in her wake. He on the other hand rarely ever forgot that pain and wore its effects like a shroud. He had shrunk in on himself and kept himself separated from others so that he wouldn't suffer the pain of loss again. If you didn't let anyone get close, they couldn't hurt you. He and Asuka did the same thing in that regard, they just did it differently.

Maybe that was why the last Angel's attack hadn't driven him insane or damaged him in some other way. While he hadn't exactly embraced the ills and bad moments of his life, he hadn't been able to hide from them either despite his best attempts. They occupied too much space in his thoughts on a constant basis and he was so used to them being there that having them dredged up by the Angel while unpleasant, wasn't debilitating on their own. It was the addition of Misato's bad memories that did the most harm but even so he was hanging in there. Just barely maybe, but he was hanging in all the same.

By the time he was done he got the feeling that he had just undergone a therapy session of his own. Considering the way his own life had progressed and all of the things he had recently learned, he had little doubt that he should probably have a reserved seat on Dr. Tokita's couch for himself. Many of those things were going through his head now as he sat in the lounge waiting for the doctor to bring Asuka out. He had wanted to prepare her for the visit first and make sure she could handle it and he had warned him that it could take a bit of time.

He felt like his head was too full of things and he didn't know how he was containing it all and not collapsing under the overwhelming weight of it all. The things that he had learned was like a laundry list for a science fiction geek's wet dream. If Kensuke knew even half of what he did now he'd stroke out in frenzy of pure otaku bliss. He could only wish that this was all just some fictional phenomenon that could be taken for entertainment purposes, but he was unfortunate enough to have the scars, both physical and mental, to prove otherwise.

As if piloting monsters to fight monsters wasn't enough of a head trip into the ether for him, on a personal level he found himself realizing that he had real and undeniable feelings for multiple females in his life. Anything related to relationships scared him to death and always had. For him just simply interacting with others was difficult enough but anything beyond that threatened to leave him paralyzed. Love was something that had been in short supply in his life yet he knew he loved Misato and she loved him, their mind trip with the Fifteenth made that an undeniable certainty. He was pretty sure that he felt the same way about Rei even if it had yet to reach the depths of what he seemed to feel toward Misato.

What he had begun to feel around Shogoki...Lilith, was truly puzzling to him. Truly, he barely knew her and until recently their only contact had been through synchronization and most of that filtered by the other soul in the Eva be it his mother or Misato. But during the time he had spent in the core with her and Misato recently it had become clear even to him that she had deep feelings for him. He wasn't exactly sure what the nature of those feelings were, but it was undeniable that they were there and he found himself feeling something in return that even in its current infancy felt very much like what he felt for Rei and Misato. Frankly, it, and the entire situation really baffled the hell out of him.

He couldn't begin to fathom how he could have such feelings for two and possibly three different women like that. That wasn't supposed to happen was it? There had to be something wrong with him, he must be pathetically needy and selfish, right? Misato and Lilith, even his mother had assured him that that wasn't the case. He had been starved for love for his entire life, starved simply for someone to truly care about him and not treat him like he was a burden or an inconvenience. Or as in the case of his father, only useful and wanted for a malignant purpose.

Just as baffling was how and why anyone was reciprocating those feelings. His mistreatment since being abandoned by his father had been planned and intentional to mould him into the tool his father desired him to be. No one was supposed to care about him, he wasn't even supposed to care about himself or his own worth. He was even made to believe that that lack of caring from anyone else was his fault. But despite all of that there was Misato and Rei and maybe even Lilith. He had to fight his ingrained instinct to distance himself from them and what he was feeling from them. It was similar to a moth and a flame, he was enticed to go to it, felt drawn to it even, but at the same time and unlike the moth, he knew he could be burned and he feared it.

As if three wasn't enough, then there was Asuka. His feelings weren't as strong for her, how could they be after the way she had treated him, but he didn't hate her and even with the abuse he had still hoped they would at least be friends. There was something there though, or at least the potential for there to be something more. He could recognize that now after discovering the truth about his feelings for the others and it did nothing to ease his angst or confusion. He was scared. Scared to accept their feelings and scared to deny them after having just a small taste of what those feelings of love and acceptance did to him. It had all the allure of an addictive drug and he feared the result of letting it take him. There was a battle going on inside of him between the desire to feel more of that and his own self loathing.

He turned to his left when he heard a soft squeak of rubber on the polished floor. Dr. Tokita was pushing Asuka towards him in a wheelchair. At first he wondered why she was in the chair until he saw the bandaging on her foot and her hands and he remembered that she had hurt herself as well when she attacked Rei. She looked far different than what he was used to. She was dressed in white hospital pyjamas and without her A10 neural clips in her hair. She looked small sitting in the chair, the usual arrogant pride that always seemed to make her presence seem larger than life was gone leaving just the scared and hurt girl behind.

Her head was up but her eyes were looking more at the floor than at him. Even so he could see that they didn't have the same sparkle to them that they used to. She looked worn and tired, nothing like her usual self. Overall the aura about her was quite familiar to him, he saw something very similar to it every time he looked in a mirror.

Dr. Tokita wheeled her up to him and set the chair's brake. "I'll be over there at the nurse's station if you need anything," he told them before walking away. He would be close enough to keep an eye on her but far enough away to give them privacy.

"H-how are you doing Asuka?" To his own ears even that sounded so lame. She had busted up hands and feet and she'd had a mental breakdown. How did he think she was doing? Reflexively he expected a harsh response.

"I'm doing okay," she said softly. "Better than I was."

She hadn't raised her head or looked at him, but she had turned just enough that he could see the fading bruise on the left side of her head. The doctor had told him about the incident so that he wouldn't be surprised by it and ask her about it.

"Um...is there anything you want that I can bring you?" He wasn't sure what that would be, her rampage through the apartment had left very little intact even among her own belongings. He had boxed up everything that was hers, destroyed or not, so that she could sort it out later if she was able. He felt that he had been tempting fate and her wrath even doing that much considering how territorial she was over anything that was hers.

"Is there anything left," she asked shakily.

"We salvaged some stuff," he answered. "I...didn't throw anything of yours away."

He didn't need to say that he had been afraid to. She knew it. "I..." she sniffled. "I broke your SDAT...I'm sorry Shinji."

He didn't miss the tears that started to roll down her cheeks. It was heartbreaking to see, he had never seen her cry about anything. "I should actually thank you for that," he said truthfully. "I can't hide from the world behind it anymore now."

He had thought about that a lot lately. That outdated player had been his biggest crutch, a wall he could hide behind and shut out the world so he wouldn't have to deal with it. All it had been was a temporary respite that he realized now had done him no good. As painful as it was to try and face reality and deal with it, to deal with his issues, he was finally learning that not standing up and dealing with it was even worse. It was a benefit of having his mother back. She blamed herself for a lot of things, but she wasn't backing away or hiding from them. He needed to at least try to do the same thing. A lot of his issues were not of his making but if he didn't try to change the direction those issues had sent him in he would be doomed to continue in a downward spiral until he hit bottom and that crash landing might be one he wouldn't get back up from.

She finally looked up at him, her watery eyes sad and pleading and her voice breaking. "W-why aren't you angry at me Shinji? I hurt Rei. I wrecked the apartment. I've treated you like garbage ever since I got here. What I did...you're the only one left to fight now. Why don't you hate me?"

There was a question that he hadn't been able to find an answer to. She certainly hadn't given him any reasons to not hate her or at least be in a state of perpetual anger with her. From almost the moment they met she had tried to assert her superiority over him. She ran him down and ridiculed him, was disrespectful and rude to him not just to his face but in front of any and all who were present. She came into his home and kicked him out of his own room with the hope and intent of getting rid of him entirely. She labelled him as spineless, an idiot, and a pervert, all conclusions she came to without even knowing anything about him. His overtures of friendship and his attempts to be helpful were all thrown in his face. She did indeed hurt Rei and left him as the only pilot capable of carrying the fight.

"I don't know Asuka," he answered, hoping he didn't sound as pathetic as she usually accused him of being. "Even if I wanted to..." and there had been times where he really did want to..."I don't think I could."

"I-I've given you every reason to," she said in little more than an ashamed whisper.

"That wasn't really you..." he began.

"But it was!" she cried. "That's who I've been for most of my life. I was so horrible to you and everyone else and I couldn't stop it. It just got worse and worse..." she stared down at her bandaged hands. "I nearly killed her. I couldn't stop..."

"That wasn't you!" he insisted, tears now leaking from his eyes. He really didn't know what to do or say but the words came spilling out of him almost on their own. Seeing people he cared about suffering in pain, especially now after what he and Misato went through with the last Angel, was something he couldn't just dumbly sit back and watch anymore. "The real you is sitting right here. The Asuka that hurt Rei is gone and she isn't coming back. It's just you now and you can be who you want to be."

"How can I do that when I don't even know _who_ I am now?" She was shaking, her bandaged hands trembling in her lap.

How could he answer that? What words could he offer her that would do the least bit of good? He was messed up too and hanging on by mere threads himself. Even the smallest of interactions with others was and always had been difficult enough for him, never mind trying to play amateur psychologist, and especially not after what he had just been through. He was more likely to say something stupid or upsetting and just make things worse.

He was about to retreat into himself like he always did, and those insufferable words _'I'm sorry'_ were about to fall out of his mouth like so much meaningless noise. They would have been that something stupid and upsetting that he was afraid of saying. He got angry with himself. Asuka needed something to reassure her, something to hang onto, not his usual weak attempt at running and hiding by apologizing for the ills of the world like he was trying to martyr himself for mankind. It was selfish. He would only be avoiding or at least delaying his own discomfort at the expense of someone else who was hurting. After a few seconds where he could practically feel Asuka sinking lower, the words finally came to him.

"After the things that have happened over the last couple of weeks I don't really think I know who I am anymore either, if I ever did," he began. "I think I finally realize that I can't keep being who I was. I don't really want to keep being who I was and I'm the only one that can change that. The world will just keep hurting me if I don't do anything. It will never get any better and I'll just keep hurting myself and the other people around me too and I don't want to do that anymore." He looked up at her and tried to smile the best that he could. "I still want to be your friend Asuka, and m-maybe we can figure out who we are and who we want to be together."

"I don't want to be who I was either," she tearfully agreed. "I don't want to be mean and I don't want to be angry and hurt everyone around me anymore." She managed a small, honest smile. "I want to be your friend too Shinji. Is there any way that you can forgive me for treating you the way I did?"

He nodded readily. "I forgive you Asuka."

She closed her eyes and took a deep, shuddering breath in relief. When she opened her eyes again however she looked rather sad again. "How...how is Rei doing?" she asked quietly.

"She's getting better," he answered quietly. "Dr. Akagi said she should recover with no permanent injuries. And she's a quick healer too I guess."

He was well aware of why that was but there was no way he could say anything to Asuka. She was in no condition to hear any of the things he had learned since his mother came back. He felt like he was lying to her even if it was just not telling her something rather than telling her a fabricated story. Rei really was healing quickly too since Dr. Akagi started cutting back on the drugs that kept her S2 organ from being active. He had seen the evidence himself how some of the fading bruises and nearly healed cuts were now completely gone after just a couple of days. The more serious wounds would still take a little longer.

"Th-that's good," she said. "I...what I did...it was vicious...I was afraid that I..."

"She's going to be okay Asuka," he reassured her.

"She didn't fight back. She didn't make a sound," she sniffled. "I don't understand. Why would she let me do that to her?"

"I-I don't know," he said quietly. "I guess that's something only she could tell you." He hated lying to her but the truth wasn't an option. Even though he did know why Rei had let Asuka do it, he still couldn't really understand it. He certainly knew about despair and feeling like he wanted the end to consume him, but allowing someone to possibly beat you to death, well, that wasn't a way he would have contemplated. He supposed that to Rei it just happened at an opportune moment.

"I'm afraid to face her," Asuka admitted. "I was afraid to face you too Shinji. I didn't want to be hurt again like I was when Momma died so I tried to put myself above and beyond everyone else. I've hurt a lot of people and wasn't very nice to even more. It was like I was trying to burn everything I walked past so there wouldn't be any consequences to what I did."

"But it doesn't work," he said knowingly. "Even if you're trying to run away and hide from everything like I was it still finds you."

"And you have to face them and the people you've hurt even if it is scary," she said. "That's something I've learned already from my sessions with Dr. Tokita. It's weird though, things don't look and feel the same to me as they did before. I guess that other part of me experienced things differently. I kind of have to learn to be me all over again. Like I'm starting my life all over again from scratch."

"That...makes a lot of sense," Shinji said. "I've kind of felt a little like that since my mother returned from the Eva."

"What's she like Shinji?" she asked. "I think I'd like to tell you about my Momma too...the good stuff, but I want to know what your Mom is like too."

Dr. Tokita smiled from his position at the nurse's station. He was just far enough away to give them privacy, but not so far that he couldn't hear their conversation. Things had gone largely as he had expected, maybe a little better even and that was encouraging. Asuka was very bright and very perceptive and in their sessions she didn't try to hide herself much to her credit. She didn't excuse everything she had ever done as being solely the product of that other part of herself and now that it seemed to be gone everything would be just fine. She was trying to own that behaviour and take responsibility for it but she worried that it would return. She did not know which part was the real her. She didn't want to be that arrogant and spiteful part, but she was aware that that aspect was and had been a part of her, was a part of the whole that was Asuka Langley Soryu.

Identifying herself and forging her core identity would be the major struggle of her recovery. The other would be coping with the still raw memory of her mother's death, which she had never really allowed herself to fully deal with. It was an encouraging sign to him then that as she talked to Shinji about his mother, she began to talk about hers as well. They had both been only four when they lost their mothers, but it seemed that she had more accessible memories from that time than Shinji did. Little wonder these children where as damaged as they were, considering how they lost the single closest person to either of them at such a young and impressionable age, and it caused him no small amount of concern considering how both children had been treated by their surviving family. He had little doubt that he would be seeing Shinji in the future as a patient as well.

He was grateful for the information he had been given by Sub Commander Fuyutsuki about both of them, he knew there was no way he would have ever gotten it from the Commander and he was fully aware of the reason why the Commander had ever even allowed him to establish this ward in the first place. For the first time since its inception he felt like he was actually accomplishing something and doing some good. For once he could actually help someone and she just happened to be one of the people who had been responsible for the fact that they were all still alive. For all that she and the other Children had been through, helping them if he could was the least he could do in repayment.

* * *

 _ **Eva Cages, Near Unit 01**_

As she made her way to the observation room overlooking Unit-01's cage, Yui couldn't help but lament that the day had turned out to be far more eventful than she had anticipated. Going down into the depths of Terminal Dogma and extracting the remaining fragments of Lilith's soul from the crucified giant should have been the extent of it, but it was late afternoon and they hadn't even gotten to that yet. Though she was grateful that the SIS people had kept her, Shinji and Fuyutsuki from being hauled in by Kiel's goons, and the meeting with them had been very productive. It would have been amusing even when Gendo was eventually brought into the room and Capt. Lake promptly punched him in the face, if it wasn't for the fact that it obviously involved something intensely personal for her.

 _'You and SEELE and your fucking Second Impact cost me the most precious thing in my life!'_ she had growled at him after flattening him with an impressive right hook. She was sure that the only thing that had kept the woman from pulling her gun and emptying it into Gendo was the large hand of her partner settling on her shoulder and subtly pulling her away. With the barest of nods from their Colonel, he had escorted her out of the room.

Even so she had enjoyed seeing Gendo with a split lip and spitting out blood...and a tooth. Too much so she felt, just as she had enjoyed tasering him. It made her wonder again about how the last ten years inside the Eva had affected her and what it meant for her going forward.

 _'Your contempt has only been directed at those who deserved it Yui,'_ Lilith reminded her.

 _'I suppose so,'_ she agreed. _'And I guess I cannot expect everything we have been through for the last ten years to have not left its mark. It would be foolish to think otherwise. Still, it does not feel right to be enjoying someone elses discomfort, even if it is Gendo.'_

 _'That just shows that even with the scars of time you are still the same kind woman you have always been,'_ Lilith said. _'The one who was able to tame me from being the beast that I was.'_

 _'Tamed you?'_ she mentally smirked. _'I would hardly call some of your actions and reactions tame.'_

 _'...I don't recall hearing any complaints, no matter what guise I was in. Pervert.'_

Ah, the benefits of a lover who had the ability to alter their body to reflect either sex and any look she desired to wear. Yui found her face going red. _'Thank you for reminding me, especially when my only partner out here is lifeless and made of rubber.'_ Lilith merely laughed. _'And mind who you're calling a pervert, she who needs to look into the mirror.'_

She sighed. "Wonderful, I'm revelling in the pain of others, them deserving it notwithstanding, and it would seem that I've become a pervert. I dare not ask what other changes the last ten years has made in me."

She took a moment to settle herself before entering the observation room and speaking to Captain Lake. If the woman was willing to tell her what had happened, she would listen. Otherwise after her outburst she might just want to have someone to talk to even if that occurrence wasn't spoken of. She opened the door and walked in, joining her at the observation window.

"I don't know whether to be in awe of that or scared shitless," the Captain drawled, indicating the purple destroyer before her. "You built one hell of a monster Dr. Ikari."

"We needed monsters to fight monsters," Yui responded. "Unfortunately too many of us became monsters ourselves along the way. And you can just call me Yui."

"Mel," she responded with a shrug. "Did you become a monster too Yui?" Lake asked.

"Even before I joined with Unit-01," she answered with a nod. "By foolishly believing in the Instrumentality Project I became just as guilty as Gendo and SEELE and just as deserving of your anger."

 _'YUI!'_ Lilith's voice echoed in her head in alarm.

"Did you know that SEELE and Gendo set up Dr. Katsuragi to cause Second Impact?" Lake asked, her voice even.

"I knew what they had found and what they were doing and I knew that as with all endeavours into the unknown that their were risks," she answered. "But I did not know until just recently that the catastrophe was deliberate."

"I'm not happy that you thought Instrumentality was a good idea," Lake said, giving her a hard look. "But if you didn't know they were going to initiate Second Impact then I have no cause to want to put a bullet in your head."

That sent a shiver down her spine, especially with the matter of fact way in which it was said. "Believe me when I say I'm not happy that I thought it was a good idea either," she admitted in self disgust. "I was still just enough of an naive idealist then to believe in such idiotic fantasy and I was so wrapped up in being on the leading edge of scientific discovery and achievement that few others could come close to that I couldn't see things the way I should have. So much so that I thought I was doing something wonderful for my son by giving myself to the Eva and somehow securing his future. I didn't quite become a mad scientist but I was certainly naively and wilfully oblivious to what should have been obvious."

"And if any of this truth escaped to the public at large it would cause large scale chaos," Lake mused. "Not to mention what the truth of humankind's true origins would do to the devoutly religious. Instead of being created by a god, mankind was seeded like a crop by aliens. That's the kind of revelation that shatters faith and breeds despair and everything bad that it can bring with it. It would make all of the strife and chaos of the last ten years look like a walk in the park."

Yui smirked. "A rough interpretation but not entirely inaccurate. At least the intent was to create life and not reap a harvest."

"Except for Kiel," she said. "Didn't think I could ever hate SEELE any more than I already did."

Yui didn't respond, waiting to see if she wished to elaborate. She noticed her looking down to the catwalk in front of the Eva where Fuyutsuki stood with Colonel McKinnley and her partner. She saw the man glance up at the window like he knew they were watching him before turning his attention back to the other two men and the Eva.

Lake smirked. "It may not look like it but he's like a kid in a candy store down there right now getting to see that Evangelion up close. Hard to believe that with some of the things we've seen and done that he can still be like that. He keeps me sane and if it wasn't for him I probably would have shot Gendo after I decked him."

"The Colonel didn't seem overly concerned about it," Yui observed.

"He knew something was bound to happen," Mel said. "Hell, knowing him that's probably why he asked to meet the Commander, just so we could get it out of the way. He knew that Matt wouldn't let me go too far. We'll be talking later and I'll apologize for my behaviour and accept any punishment he deems fit for me. It was pretty unprofessional of me."

"Even if it did feel pretty good to deck him?" she guessed, a slight upturn coming to her lips despite her best efforts to not do it.

"I thought it would but it felt pretty hollow actually," she admitted. "And it doesn't solve or fix anything." She paused for a moment, thinking. "My younger brother Ron was fifteen when Second Impact happened. He was on a school trip to Florida when the tidal waves swamped the eastern seaboard and completely submerged the entire state. He was the only member of my family who had my back and hadn't disowned me. He meant the world to me."

"What happened with your family if you don't mind me asking?" Yui said quietly.

Mel shrugged. "I wouldn't bend to their will. They're rich business people and wanted me to follow in their footsteps. Wanted me to marry some rich ass whose father ran another large company to tie the two together. Had it arranged since I was old enough to walk. They had visions of building a massive business empire and wanted to use their kids to help them acquire it. My sister was all for it but I couldn't stand the thought of working in an office tower all my life or being married off like that, especially to someone I couldn't stand the sight of. As soon as I was old enough to enlist without their consent I did what I always wanted to do. I joined the Army."

"I take it that didn't go over well?" She could only imagine. She had known a few families here in Japan that still did things in the way of the old clans and going against the clan's wishes was always an ugly prospect.

"They were mad as hell, saw it as a black eye to their reputation," Mel said with a smirk. "Got worse when they discovered that no matter how much they whined or yelled at me and no matter how much influence they tried to exert through their elite circle of friends, which included several politicians and military brass, they couldn't force me out. Got even better when I was accepted a couple of years later for Special Warfare training. Ron though, he was cheering me on the whole time, backed me all the way when the rest of the family turned their backs on me and disowned me."

"During that training, was that when you met him?" Yui asked, gesturing to her partner.

Mel shook her head. "Nope. Didn't meet that overgrown bull moose until the Colonel recruited us and we both ended up attached to the UN military and with the SIS. Matt's from Canada, comes from a military family with a long history and lost them all in the Impact. He was in a SpecWar unit too when the Colonel recruited us. We got along pretty well and worked well together right away. Nobody I'd rather have watching my back than him. We've been through a lot together."

' _Think I should let him in?'_ Lilith asked. Yui looked to see that Captain Riker had walked up the ramp the pilots used to access the plug and was taking an up close look at Unit 01. _'He looks like quite the catch. Misato agrees.'_

' _I don't think Captain Lake would appreciate that,'_ Yui thought back with a chuckle.

Lake saw the amused look on Yui's face and followed her gaze. She smiled and shook her head. "I am so going to give him the gears later about this."

"You seem rather fond of him," Yui observed.

She shrugged again. "Neither of us has much else to hold onto besides what we do for a living and that isn't something you want to hang onto exclusively. You need something to help you hold onto your humanity and keep you sane. Something to remind us why we do what we do. He's better at it than I am, like he has a switch he can turn on and off. Me, I'm too much like Katsuragi and have a tendency to try and drown things in beer and I need someone to keep me on track."

"Do you know Misato?" Yui asked.

Mel nodded. "Met her in Germany while I was training with a counter terrorist unit of theirs we had worked with a few times. It was a sort of rehab for me, I was just coming back to active duty after getting shot a few months before. We thought we were closing in on a big shot from SEELE but it was a set up. I got shot in the back and the big bear down there got angry and took the guy apart with his bare hands. Didn't find out until later that he took one in the side. Dumb ass nearly bled to death getting me help. After the days training I would go out to the bar and I ran into Katsuragi one night. I was there for a couple of months so we ran into each other a lot. We became drinking buddies and drank most of the others under the table. We also gave each other someone else to confide in. We're both a little messed up I'd say."

"Seems to be a precondition to being tied up with anything involving this place," Yui sighed. "Then again, that's what people like Gendo and Kiel were counting on. It makes people easier to manipulate."

"I suppose when you're trying to end the world it doesn't matter who you twist and use along the way," Lake mused. She turned away from the window and started for the door. "At least now we have a real chance to stop this freaking nightmare. Maybe then we can finally start fixing the world instead of trying to destroy it."

* * *

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	21. Chapter 21

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

 **Transposed**

 _ **Chapter 21**_

By elevator, it was a long trip down to the bottom of Terminal Dogma. It was even longer when going down by the cable lift that Unit 01 now rode. There was little light in the shaft except when passing the openings of the various levels and even less worth seeing when there was light. It was doubtful that Yui would have seen much of it anyway if there were, being as deeply into her thoughts as she was. She was dressed in a predominantly black and blue plug suit and sitting on Unit 01's left shoulder, tethered in place by a safety line hooked to a magnetic clamp that was stuck to the shoulder pylon.

Shinji had turned pale when he saw her in the plug suit, a flash of his recently assaulted memories returning him to the last time he saw her in one, the day she was absorbed by the Eva and the downward spiral of his life began. She crushed him into a hug and assured him that nothing was going to happen to her, that she was not going anywhere. Nothing could ever make her leave him again. Every time she saw the traces of doubt or fear or dejection on his face, it was like pins being stuck in her heart, like she was some living voodoo doll. Problem was, at the root of it all it was she herself that was the cause of it.

The plug suit was pretty much necessary because she would need to sync with the Eva after extracting the last of Lilith's soul from her seed body and transferring most of it back to her in the core. She hadn't even thought about it affecting Shinji at all. She should have considered that it might since it was probably his worst memory right along side Gendo abandoning him, especially since the last Angel had turned what was an old, hazy memory into something that was now new and fresh again. At least she should have told him before hand to prepare him for it. That was only part of what was occupying her thoughts.

"Mom, is everything okay?" Shnji's concerned voice sounded loud and clear in the earpiece she had in her right ear.

"Sorry for being so quiet Shinji, my mind was elsewhere," she answered.

"What...what were you thinking about?" he asked timidly, fearing that he was prying.

"The cost," she said as she leaned back against the pylon. "Hearing what Capt. Lake and Capt. Riker lost because of Second Impact. Hearing at dinner that Colonel McKinnley lost his wife and daughters. It made me realize how little attention I had really paid to what happened to the world in that disaster."

"What do you mean?" he asked.

"After it happened I was certainly aware of the enormous loss of life and the damage it did to the planet," she began. "Everyone either lost someone or knew people who had lost someone, or both, and I was no different. Yet I was so busy with my work that I was insulated from the true day to day reality of the world, it somehow seemed to be all in the background. I was part of an organization that caused it as it turned out, yet I never truly concerned myself with it. Then I removed myself from it entirely by letting the Eva take me."

"But you didn't know that it wasn't an accident," he offered. Maybe he was being wilfully blind and naive about the role she had played in everything, but he hated to see her piling blame on herself.

"I didn't," she admitted. "But I can't help but think that if I had it may have changed my thinking and I would have done things differently. Maybe I would have blown the whistle on what SEELE was doing. Maybe I could have found another way to make the Eva work. If I had, your life would have been better. You wouldn't have suffered so much."

"But you are here now Mom and that alone makes my life better," he said, a smile now evident in his voice.

"And I should have been here all along," she said. "But I developed tunnel vision, I was absolutely convinced that what I was doing was right when it was anything but." She shook her head in disgust. "A great many of the projects that myself and NERV as a whole were working on could have had immense benefits for mankind. The medical benefits alone would be staggering. It is horribly ironic that some of the greatest scientific and technological achievements of mankind have often been born from warfare and destruction. We could have been doing so much good for the world."

"Dr. Tokita said something to me before I visited Asuka," Shinji said. "He said, _'you can't go forward if you keep looking back. Remembering the past is helpful. Living in it isn't'_. When this is all over and we don't have to fight anymore, you could still use all of those things to help people."

"I suppose I could at that," she answered with a smile. ' _Just like Mel said, maybe then we can finally start fixing the world instead of trying to destroy it.'_ "But before we can get to that, we've got things to take care of to help better our chances of getting there."

It was several more minutes before they reached the bottom of the shaft where they were then confronted by a huge set of rusting doors.

"We're here Professor," she called over her comm set. "Can you open the doors please?"

Up in the command centre Fuyutsuki nodded to Dr. Akagi who tapped in the security override code for the MAGI to open the doors. "The command has been sent."

"They're opening now," she acknowledged.

With first the heavy 'thunk' of several locking bolts retracting, then an ear splitting shriek of little used gears and servos, the massive, thick doors slowly ground open. It took a couple of minutes for it to open enough to let the Eva pass through.

"Whoa," Shinji gasped as he saw the huge pool of LCL and a white giant wearing a seven eyed mask that was crucified to an enormous red cross at the end of the room. More of a half a giant actually since it was missing its body from the waist down. Stabbed into the middle of its chest was a long, purplish coloured, two pronged spear. The shaft of it looked like two separate pieces that had been twisted around each other.

"Each Seed is accompanied by one of these," Yui explained. "It's a fail safe should something go wrong with the Seed or if it should act in a way contrary to its purpose. There should be another somewhere on the planet but it hasn't been found."

As instructed when they had gone over it earlier, Shinji walked Unit 01 through the LCL pool and up to the Lance. Taking a firm grip on it with both hands he slowly pulled it out of the giant. The moment it left the body, the flesh at the waist bulged and suddenly reformed the giant's legs.

"What the...!? he exclaimed, taking a quick step back.

"It's okay Shinji," she assured him. "We expected that might happen, there's nothing to worry about." She stood. "Now, I need you to put me close to the body."

"O-okay," he said nervously, not really wanting to put her anywhere near it. Holding the lance with the left hand, he raised the right hand until it was at his left shoulder. Yui disconnected the magnetic clamp, hopped into the palm of the Eva's hand, and reengaged the clamp again.

"Okay Shinji, nice and easy," she instructed calmly.

Slowly and carefully he moved the arm until the hand was nearly touching the giant's pale flesh. Yui ventured forward onto the Eva's fingers and knelt down. Taking a deep breath she extended her hands.

"Here we go."

Doing the same as she had with Rei, she used the bit of Lilith's soul that had been given to her to draw on the soul energy within the giant body. She expected a slow and steady flow like she got from Rei, but instead it was like a torrent rushing into her, so sudden and so much that she couldn't utter a sound in her shock nor could she pull away from it and break the contact. The energy rushed into her like it was seeking to be reunited with more of itself and it would not be interrupted until it did so.

It was overflowing and overwhelming her mind, her body, and her soul. It crashed through her like ocean waves and burned like fire, threatening to consume everything that she was and leaving her awash and shaking in equal parts of pleasure and pain. Her senses were sharper than she had ever known and she felt like her consciousness, her very soul were expanding. She didn't feel the flow end when it finally stopped entering into her, she was barely aware of anything as she lay writhing in the Eva's palm in a mixture of agony and ecstasy.

She didn't hear Shinji's panicked voice as he called to her. The sound of panicked voices from the command deck in her earpiece was an incomprehensible buzz. She barely heard Lilith's voice in her head as she tried to get through to her. She didn't realize that Lilith had established a three way link with Shinji to remain in contact with her while she guided the nearly hysterical boy through the extremely awkward task of trying to get her across the Eva's back and up into the entry plug.

She knew nothing again with any sense of self or clarity until sometime later when she began to awake as if from a deep yet tumultuous sleep. She was exhausted and felt a little like a burned out shell with a side order of post orgasmic bliss. She felt worn to the bone. She was disoriented when her eyes slowly opened to a world of ever changing colours and it felt like someone or something was wrapped tightly around her. Her senses were still muddled enough that she couldn't tell which.

"Yui," a voice spoke softly into her ear.

"Hmwuh," was her mumbled response.

"Yui, take long, deep breaths," the voice said. "Focus your mind. Concentrate on something, a strong image or something you hold dear. You need to stay focused on that and regain yourself."

A strong image. Something she held dear. Shinji. Her precious little boy. The son she had wronged so badly but who forgave her and didn't place any blame for the ills of his life upon her even though he had every right to. She loved him so much, had missed him so much and she had missed so much of his life. She loved him more than anything but had wronged him so badly.

But still he loved her. His face almost literally lit up whenever he saw her and he cherished every moment they got to spend together and she felt very much the same. How great it had been even just the previous night when she enjoyed the wonderful meal he made for her with so much love and pride, and to hold him as they sat on the couch and watched a movie. Every instance of happiness made her despise what she had done even more, even as she craved to be part of it and to be the cause of it for him.

She pictured his shy smile and the adoring look in his eyes and held onto that image. If he could love and forgive her then maybe she could eventually learn to live with what she had done. So long as he did and so long as she could love him and make his life better she had a chance. He was her anchor now, her reason for everything and nothing else was as important.

"Good Yui," the voice said. "Keep it up, you're almost there."

Clarity and focus began to return to her mind. She recognized the shifting colours now as the transition space between the entry plug and the core. She realized that the who or what that was wrapped around her was Lilith, the sight of the light brown skin and dark hair of the form she seemed to have a preference for now confirming it. Off to her right she saw Shinji being held by Misato. He looked so worried and afraid, like he was going to lose her all over again.

"Shinji," she said softly, managing a tired smile.

"Mom!" He bolted from Misato's hold and caught both her and Lilith with his desperate embrace. Misato followed and stood behind him, her hands resting on his shoulders. She had been really worried about him. Not knowing what was happening to his mother had put the poor kid in near hysterics and she had done her best to keep him calm.

"It's okay Shinji," Yui assured him. "I'll be fine. I am fine, just really tired." She also ached all over and had intermittent spasms rocking her body, like she was being hit all over with little jolts of electricity.

"What happened?" he asked, unable to control the flow of tears that overtook him again. "I was so afraid that I was going to lose you again."

"It's my fault," Lilith said, separating herself from Yui enough to be able to look at them both. "The remnant of my soul within that body was larger than I thought it would be and it seems that there was a fragment of my consciousness still attached to it."

"You couldn't have known," Yui said. "Not with the Lance in place."

"I should have accounted for that," Lilith countered. "At the very least I should have tried sensing it after Shinji removed the Lance. It very nearly tore your mind and soul apart."

"Then we are both to blame because I didn't wait," Yui said. "I was impatient about finally getting this done and taking another option out of Gendo's hands."

"You know, all of us have spent a hell of a lot of time trying to take the blame for everything around us," Misato interjected as she wrapped her arms back around Shinji and let her chin settle atop his head. "Don't you think we've all wallowed in it and tried to play the martyr just about long enough?"

Yui sighed, feeling even more tired than she already was. "You're right. No matter what we may be guilty of we aren't going to change it or atone for it by feeling sorry for ourselves. And if we don't stop SEELE and Kiel, then it won't matter anyway."

"So instead of guilt trips why don't we give some much needed credit where it's due," Misato suggested. "You saved your Mom's life Shinji. You got her into the plug in time for Lilith to take that part of her soul back before things got _really_ bad."

"My little hero," Yui smiled with a bit more energy. "I guess I owe him big now."

"Despite how scared you were you did well Shinji," Lilith told him.

"Oh...um, I h-had to do something," he stammered, obviously uncomfortable with the praise.

"And I'm glad you did," his mother said as she laid her palm against his cheek. "Thank you Shinji."

"The two of you should get back to your bodies now," Lilith said after a moment. "The Eva will be back to the top of the shaft soon." It was true, but there was still time. She was trying to save Shinji the angst of seeing his mother in the nude again. Now that he was calming down it was clear by his demeanour that he had belatedly noticed. She certainly didn't mind the sight herself, Yui was rather attractive and nicely put together. At least this time the problem wasn't caused by Yui herself for forgetting to get dressed. She rather liked teasing her about that.

Misato smirked. "Ritsuko will be waiting for you. Just think of all the wonderful tests you'll have to go through before she's satisfied that you're okay. Shinji can relate."

"Please don't remind me," he groaned.

Yui sagged noticeably. "I suppose I couldn't just stay in here for a while?"

"You'd only be giving her more time to thinks of things to test you for," Misato answered, laughing.

"Wonderful." Being a scientist herself she could only imagine what she was in for. "Might as well get it over with then." She took Shinji by the hand and they both faded away, back to fully rejoin their bodies in the entry plug.

* * *

Shinji was sitting in the pilot's seat with Yui sitting across his lap and leaning heavily against him in a half hug, half slump.

"My body feels like it's made out of rubber," she complained. "Very soft, flimsy rubber at that."

"Are you really okay Mom?" he asked, obviously still worried.

"Nothing that food, a bath, and sleep won't fix," she answered. "And I don't even care what order they come in." She looked up at him and smiled, her hand rising to caress his face. "Again, thank you Shinji."

"I just got you back Mom, I couldn't lose you again," he said, hugging her.

"And you won't," she said. "I promise." She smiled again. " _We_ are going to save the world and _we_ are going to live happily ever after." She knew how corny it sounded but she didn't care.

"I really hope we can," he said.

"We will." She yawned. "You don't mind if I take little nap before we get back topside do you?"

He didn't of course and she was practically asleep before he answered.

* * *

 _ **NERV-3 Germany, Dummy Plug Lab**_

Scientifically speaking, the workings of the Dummy Plug system was a brilliant stroke of genius. The ability to download the memories and experiences of one being into the mind of another. The fact that it was absolutely illegal had meant nothing to people like Gendo Ikari or Lorenz Kiel, or any of the scientists that had eagerly worked on the project for them. Also never mind that the vessel to receive said memories and experiences was a clone of the one giving them, and that cloning was also highly illegal. Of course so was trying to destroy the human race for various and sundry selfish purposes, but what's a few billion deaths and the complete genocide of entire race so long as you get what you want out of it? It's not like there would be anyone left to level legal charges against you or take revenge once it was all said and done.

In Tokyo-3 the unfortunate one who got to impart their memories and experiences to a batch of clones was the container of Lilith's soul, Rei Ayanami. The subject at Berlin, who was currently occupying the LCL filled glass cylinder of the memory transfer machine, was the container of Adam's soul. A teen male with pale skin, red eyes, and grey hair who went by the name Kaworu Nagisa. He was also Tabris, the Seventeenth Angel. However, he wasn't looking too animated at the moment. There were a couple of probes stuck into his head and one in his abdomen that was piercing his S2 organ. His eyes were glassy and he had the sagging body posture of someone whose brain was no longer capable of voluntarily controlling their body. He had been in the middle of a download session when he suddenly went rigid and gasped, _'the call...it has stopped'_ , before going limp and motionless.

Several yards away across the cavernous room was a large semi circular control console and desk, its top littered with scanning equipment, monitors, binders, and notebooks. Behind it all, scrutinizing data on one of the screens was Lorenz Kiel and his chief scientist, Dr. Gerhard Holzer. Holzer was a thin, pale, bald headed man who looked more ghoul than human. Many who worked around him quietly referred to him as a modern day Dr. Frankenstein. All he needed to complete the look was a disfigured, hunchbacked assistant named Igor and he'd be all set. When their subject went motionless, they wasted no time in taking advantage of it.

"You're not looking so good their Kaworu-kun," a girl's voice teasingly spoke.

No one could see or hear her as she literally stood in mid air, hands on hips, and facing the body in the elevated tank. She looked to be in her mid teens with dark brown hair that hung to the middle of her back in twin tails. Her green eyes held a spark of mischief to them and were shielded by a pair of oval red rimmed glasses. She was quite well endowed for the look of her age and was wearing an untucked white Oxford shirt with a dark green tie over a red and green plaid skirt, black thigh high stockings, and brown loafers.

Her name, the name she had adopted after coming here was Mari Makinami. Mari _Illustrious_ Makinami. Illustrious because, well, she thought it was an interesting thing to call herself and it just seemed to fit her somewhat boisterous personality. Besides, she had never had a real name before coming here and it was awkward and depressing for both her and those she answered to, those who had saved her and given her a life and a purpose, to continue to call her by the number of the experiment that created her. Seven seven seven zero seven, or Seven for short, was a reminder of how much she had endured. It had been okay for a while but as she progressed and by the time she was sent for this assignment she wanted a real name. She wanted a real identity all her own.

After arriving here ten years ago she began crafting that identity for herself so that she could live among the people. Sure, she could move among them and remain unseen, but even so she still needed to eat and sleep and remaining intangible could get tiring, especially for the mind. Never mind the toll several teleports to different locations around the world in a day could take. Being able to become tangible and interact and live normally for a few hours a day was good for her and she enjoyed a good meal, a hot bath, a nice soft bed, and the comfort of having a home to go to just as much or more than any other human did. Being alone sucked but there wasn't much to be done about that right now.

But despite how she looked she was no more human than either Tabris or Kiel himself. She was a Watcher, sent here by Kiel's peers shortly after Second Impact to watch, observe, and report on what was happening on this world and what his role in the disaster had been, if any. With the ability to remain unseen unless she wished to be seen, it was easy for her to gain access to anything, anywhere. It didn't take long to discover what had happened but it took a few years of diligent digging and listening to fully discover Kiel's plan. She had hoped that the result of her findings would see her given the go ahead to take Kiel out but that didn't happen, much to her annoyance.

She had been told that she had to remain unseen and let things run their course. The Children of Lilith had ingeniously created the means to defeat the Children of Adam and thus they had the opportunity to stop Kiel themselves and should be afforded that opportunity. She was not to take direct action against him until either his plan was defeated or its success was imminent, then she could do what needed to be done to stop him and preserve the lives of the Lilim. She didn't particularly like those orders, she felt that he should have been taken out when she first discovered what he was doing, but she had to do as she had been instructed. Overall, it wasn't easy for someone who liked to get in on the action and break a few things.

"Of course, you were going to end up like this anyway," she told the Angel. "He has more use for you like this than he ever did when you were aware and awake. He never liked the whole _'Angel of Free Will'_ thing either. It gave the potential for you to take actions he couldn't fully account for or control." She looked over her shoulder at Kiel, a disdainful look on her face. "Free will is an impediment to his plans, he can't let something like that go unchecked, so here you float with probes in your brain and in your gut." She looked back to the tube. "Personally, I always did think you were kind of creepy. I mean, I can understand your interest in learning about the Lilim, but your fascination with Shinji-kun gave me the freaking shivers and not the pleasant kind either." She lowered her gaze slightly and smirked. "And for such a superior being, compared to Shinji-kun you come up a little short there 'container of Adam's soul'. Thankfully Shinji will never have to experience your special brand of weird."

After she was done here she would go to Tokyo-3 and check in on Shinji, he was someone whom she had gained a great affinity for. When she first arrived here the earliest part of her investigation was to find out what had caused Second Impact. Once she did that and found that Kiel was involved her next job was to track down and identify all of the major participants in his plan. During that time she had of course learned of the events of Yui Ikari's demise and even worse how Gendo Ikari had reacted to it. When she learned that the man had taken his four year old son, who had just lost his mother, and shoved him off on someone else who didn't really want anything to do with him...by just leaving him at the train station no less, she very nearly lost control and killed him on the spot.

Instead she teleported away, ended up in the middle of some border war in Africa, and in a screaming, anger laced display of her power, eradicated the majority of the armies of the warring sides to the point that neither could or wanted to continue. The site still bore the scars of her anger to this day. The only reason her handlers let her get away with it was because they felt responsible for the plight of the people of Earth since Kiel was one of their own and they had already been through so much. Ending a war that was only bringing more misery to them was a good thing. It was a huge change in attitude for them, a sign that even a race as ancient and evolved as they were could still be flexible in their thinking and come back from their previously arrogant and aloof ways.

She found where Shinji was living and it saddened her to see the state the child was in. He was horribly lonely, having few if any friends and his guardians treated him like a burden and spent the money they were given for his care on themselves. He practically had to fend for himself, learning to do household chores like cooking, cleaning, and laundry. Doing these things and doing them well seemed to earn him a little less animosity so he became very good at it. It was the beginning of his quest to seek approval through pleasing others by doing as they wished him to do.

She had been there when he stood before Unit 01 and met his father and when he fought his first battle. She was there when Misato berated him after his second and she followed him when he ran off and wandered the city. She fumed as the Second Child arrived and treated him as something beneath her notice. She bore witness to all of his battles and sat by his bedside when he found himself in the hospital.

She stood by shaking in rage as he was lost within the Dirac Sea of the Twelfth Angel and NERV's only response was to wait until the last minute then bombard it with every N2 bomb they could get their hands on. It took every ounce of restraint she had and then some not to manifest the weapon that was a part of her very soul and destroy the Angel herself and set him free. As it was she had grinned like a maniac when a roaring, blood soaked Unit 01 tore its way out of Leliel and back into the world.

That restraint would break entirely however when Gendo Ikari used the dummy plug to take control from Shinji and make Unit 01 tear apart the Angel infected Unit 03. At several different locations around the world that day, several small hostile armies, terrorist units, and Angel worshipping cults met bloody and explosive ends. Utterly drained after her rampage she joined Shinji in his isolation cell and stayed with him until he was released. She didn't dare follow him to his father's office because she didn't trust herself not to murder the man on the spot. She witnessed his battle against the Fourteenth and was there when he and his mother emerged from the Eva's core.

She hadn't been there when he suffered the attack of the Fifteenth, she had been pretty busy keeping track of all the chaos within SEELE as one of their most prominent members was assassinated and the UN's Black Op's team began to start tearing into the organization now that they finally had proof of what they were up to and who to go after. Luckily she happened to be there when Yui, Fuyutsuki, and Akagi wrested control from Gendo and took the fragment of Adam from him. She was shocked to learn just what was within Unit 01, but was happy to know that it looked like they had a growing advantage over Kiel.

She floated over to where he and Dr. Holzer were studying the data on their now shackled Angel and stood on the edge of the desk. She bent at the waist and looked down at the wheelchair bound man, pulling down her right eyelid and sticking her tongue out at him.

"You shrivelled up old bastard," she all but snarled. "You and your plans are fucked and you don't even know it. You still think you have the upper hand and I am sooo going to enjoy the look on your face when you realize you're done for."

With that said she hopped off the desk and wandered out of the lab, now happily humming to herself. "Hmm, maybe I should go prank one of the Committee members before I go check on Shinji. Haven't done that in a while. They're all so paranoid right now that they almost literally jump at their own shadows. Ah, I haven't visited Petrov in Moscow recently, I think I'll go drop some laxative in his Borscht. Should do wonders along with the quart of vodka he'll put away after dinner."

In the blink of an eye she was gone.

* * *

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	22. Chapter 22

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

 **Transposed**

 _ **Chapter 22**_

While she had never been trampled, drug over rough ground, and tossed down a flight of stairs, Yui Ikari could say with some certainty that it must feel very much like she did right now as she slowly awoke.

"At least now I know who Shinji inherited his penchant for winding up in the hospital from," the mildly amused voice of Ritsuko Akagi said from somewhere close to her right.

"Ha ha," Yui groaned as she rolled her head to squint at her tormentor. Ritsuko was sitting in a chair next to the bed, a laptop across her knees. Next to her was a cart full of monitoring equipment and numerous wire leads were running from it to the bed and were stuck to various places on her head. She frowned at the sat up. "Misato warned me about you and your fiendish testing fetish."

"Did she now?," Ritsuko smirked. "And I wanted the floating naked in a tube of LCL to be a surprise."

Yui mildly glared at her. "If you're expecting to dent my modesty I lost that by spending the last ten years naked in my soul form inside the Eva."

"I guess we'll have to leave the embarrassed reactions to Shinji then," she lamented.

"Speaking of Shinji, where is he?" she asked.

Ritsuko point across the bed to Yui's left to another bed where Shinji lay sleeping. "And before you go panicking, he's fine. Or at least he should be. He was a wreck. When we brought you out of the Eva you didn't wake up. He wouldn't leave your side and he was literally worrying himself sick. I gave him a little something to put him to sleep."

Yui sighed. "He's so afraid that he's going to lose me again."

"It'll be a while yet before he wakes up but by then he'll be able to see for himself that you're fine," Ritsuko said.

"So then what's all this?" Yui asked, gesturing to the equipment beside the bed.

"Verification," Ritsuko answered smugly. "And research. Once Shinji got you back into the entry plug we began to get brainwave readings from you and what we saw was something that exceeded normal human wave patterns." She closed off what she had been doing on her laptop and began bringing up the scan results. "What we saw indicated a much higher level of brain activity and in zones that suggest a higher percentage of the brain's capacity was active." She turned the laptop around so Yui could see the screen. "And the current readings, while not nearly as high, are still higher than the norm. I compared them with your previous scans. The results from your return from the Eva after ten years were a little higher than before you went in, and these results are even higher."

"That's not really surprising," Yui commented. "While Lilith is not one of the First, she is a life form created by them to bring life to other worlds and is a higher life form compared to those she created. The human mind cannot handle being exposed to her consciousness in anything but small amounts. To make the Eva work and to protect its pilot, I had to be in some small level of mental synchronization with her. The result was a small expansion in my brain function."

"Then that is what happened again when you took in the remnants of her soul within the Seed body?" Ritsuko surmised.

"Pretty much," Yui answered. "And maybe a little more. There was more of her soul remaining in that body than we thought and apparently there was still a shred of her consciousness attached. As soon as those remnants came into contact with the small bit of herself Lilith gifted me with it all rushed in to me. I felt like my mind and my soul were being stretched."

"Judging by your reaction as it was happening it must have been excruciating," Ritsuko said.

"Equal parts agony and ecstasy," Yui said. "Think about the greatest orgasm you ever had and multiple it several times. Then take the absolute worst hangover you've ever had and multiply that several times, then add them together. Then double it."

Ritsuko paled. "That certainly explains your vitals signs after you got in the Eva. Everything was spiked very high, I honestly don't know how you didn't end up having a stroke or how you didn't go into cardiac arrest."

"I think I was in more danger of losing my mind, my sense of self," Yui said. "As it was I nearly did. My mind and soul was being overwhelmed and I nearly lost all sense of who and what I was."

"It's a good thing Shinji got you into the plug when he did then so Lilith could take back what you had absorbed," Ritsuko said.

"It took more than that," Yui continued. "Even after she did I was still lost. I was barely comprehending anything. She told me to focus on something. A strong image, something I hold dear." She again turned to the bed where Shinji still slept. "I focused on him. He has every right to despise me as much as he does his father, yet he doesn't. Even if the rest of the world were to hate my guts, he still loves me and that's the only thing I truly need. He is the anchor that kept me from drifting away."

"I think Maya is becoming my anchor," Ritsuko said with a wry smile. "I practically used to be her at one time. I was shy and unsure of myself in the world at large, a lot of that had to do with living in my mother's shadow."

"Knowing Naoko as I did, that couldn't have been easy," Yui said.

"It wasn't," Ritsuko agreed. "I thought I was stepping out of that, that I had become important and wanted, but really I was only just a means to an end to Gendo. Something he could use however he wanted to. I despised Rei for garnering so much of his attention and I despised you for being his only focus, only to then fear you when you returned for what you would think of me. I was walking a very ragged edge and wasn't liking what I saw anymore when I looked in the mirror. I couldn't even fool myself any longer into believing I was a victim since I was complicit in my own downward spiral. I was headed for a bad end."

"I didn't help things when I told you what was really going on," Yui began. "It was rather vindictive of me to do it that way, dragging her in like that. I had been back long enough to see how she looked up to you. I'm guilty enough for my participation in all of this, I had no moral high ground to stand on but acted like I did."

"It was probably good that you did do it that way," Ritsuko said. "It allowed her to see me for what I really was, what I had become, and make up her mind for herself. Even with me sitting at rock bottom and all of my faults and deeds exposed she decided to stand by me and help me stand back up. I'm sure I don't deserve it but I want to hang onto it and not let go."

"Then don't," Yui said with a shrug and a smile. "Hang onto it for all it's worth. From what I've seen she wants you to lean on her, she wants to be there for you. It will be good for both of you."

"I guess then for the first time in a long time I'll actually have something to look forward to," Ritsuko said hopefully. She grinned evilly. "Besides, that is, putting you through a whole bunch more tests."

"I should have stayed in the Eva," she sighed.

* * *

 _ **Command Level Conference Room/Temporary SIS Command Centre**_

"Now that we have some idea what SEELE was planning, it makes the design of this place obvious," Col. McKinnley said as he looked over the holographic display model of NERV's Tokyo 3 facility. "When we first looked at the plans it was blatantly obvious that this place was not laid out to be defended from any kind of a military attack."

"The UN Oversight Committee was likely stacked with their loyalists or people they bought," Fuyutsuki offered. "I don't even recall hearing any noise being made at the time it was constructed about such defensive deficiencies."

"The internal investigation back at UN HQ has only just gotten started," McKinnley said. "But my people have already found the late Harold Connelly III chaired that committee and he most likely would have hand picked the members and had them rubber stamp everything." He eyed the map critically. "There are so many ways in they might as well have just put up a big neon sign that said 'invade us'. Even with the full security complement listed for this base, you still wouldn't be able to adequately watch and protect every entrance and keep a determined foe out."

On the map all of the main, public street level entrances were marked in red. Secondary entrances and covert entrances accessed through certain buildings were marked in yellow. Classified entrances used by NERV Security and Section 2 were marked in green. Overall, there were dozens of these colour coded entrance and exit points all over the city, and that didn't include all of the maintenance doors and hatches in building sub-basements that allowed crews to maintain and repair the mechanisms that raised and lowered the buildings. These were all marked in dark blue. The massive egress points for the Evas were marked in white.

"These are just the exit and entrance points that we know about," Fuyutsuki said. "It wouldn't surprise me if there were others that were temporary from the construction period but were never properly closed and sealed."

"The Evangelion hatches and the main entrances are built like blast doors," McKinnley said. "So they would be the hardest to get through. The Eva hatches need to be usable at a moments notice but we can limit the number of the red entrances to as few as possible and have an armed contingent on hand instead of relying on access cards and cameras."

"The ones not being used can be locked down easily enough," Fuyutsuki said. "Maintenance crews can weld the yellow entrances shut easily enough but there are simply too many in blue to deal with and they are vital to keeping the building lock down and lowering mechanisms functioning."

"What about these doors marked in a lighter blue?" McKinnley asked.

"Those are the internal doors that lead into the sub-floors where those lock down and lowering mechanisms are located," Fuyutsuki answered. "There are fewer of them than the dark blue ones that access the building basements."

"Then those are the ones we should try to lock out then," McKinnley said with a nod. "I know that access still needs to be possible for maintenance, but at least we can lock those down from the inside and control access to them better."

The door to the conference room opened and Lake and Riker walked in. Both were dressed as they had been the day before, minus the windbreakers. Riker carried a pistol strapped to his right thigh and one holstered under his left arm, Lake had a pistol strapped to either thigh.

"How did it go?" McKinnley asked.

"We rounded up the last two stragglers we identified as SEELE moles from Section 2 and the security force," Lake answered. "They're on their way off site now to join the rest in our lock up in Tokyo 2."

"Any trouble," he asked.

"Had to dent one of them up a little when he got uncooperative with me," Riker answered with a shrug. "No shots fired and no bloodshed."

"Was kind of funny," Lake grinned. "Looked like Rocky Balboa beating a side of beef, only with less effect. A thump on top of the head and the guy was down and out."

"Sorry I missed it," the Colonel said. "I could have used a chuckle."

"That bad?" Lake asked.

"Worse," he answered. "We can control the main entrance points, but there are too many others to be monitored or controlled in any kind of effective manner. The biggest problem is the level that contains all of the machinery and mechanisms to raise and lower the buildings and the maintenance access ways to it. Stopping and enemy from getting into this level is almost impossible. I'd like the two of you to go over this and see if there are ways we can minimize the points of entry from this level into the rest of the base." He looked at his watch. "The Sub Commander and I along with Mr. Kaji have a meeting with the Prime Minister and Kaji's handlers. Hopefully we can also set up a holographic conference with the UN Secretary General while we're there and get a few things ironed out."

"Won't be easy but we'll come up with something," Riker said.

"You always do," McKinnley said. "Even if all we can do is slow down anyone who gets in it might be enough."

"You have my apologies," Fuyutsuki added. "Gendo knew how vulnerable this facility was to human attack, yet he was unconcerned with it. By that stage he would have had the wheels in motion for Third Impact and any attack on the base would have been irrelevant."

"Actually I think we're getting the better detail here," Lake smirked. "You have to go meet with politicians, we'd rather face a near impossible security planning issue any day."

"It would be interesting though to see the look on the Prime Minister's face when he finds out that one of his most trusted Ministers was helping to plot the end of the world and was using him to help do it," Riker mused.

"And that is where a great deal of leverage for us lies," McKinnley said. "I'll check in with you when we get back."

As he and Fuyutsuki left, Riker picked up a tablet from the table that was showing the same schematics as the big holographic screen. Using it like a remote he changed the view to the building retraction mechanical level. He sat on the end of the table and studied the big screen. He had looked over a lot of the base plans shortly after they got the information package form Kaji so he was at least somewhat familiar with it. A moment later his partner sat to his right, handing him a bottle of water. They remained quiet for a while as they looked over the plans.

"Place is a veritable sieve," she said, finally breaking the silence. "There's no way possible to keep anyone out of here who is determined to get in."

"If the buildings are retracted and the bulkhead doors over them are closed, that eliminates the entry points from the buildings themselves," he said. "But that would also require evacuation of the city, not that there are many people left here anyway besides base personnel. I think that leaves each block with a concealed hatch for top side access if it's needed. Shouldn't be too hard to weld those shut, but there are a lot of them."

"That would delay an entry attempt but even so those hatches are a weak link and could be blown back open," she said. "They would give up chances of a quiet entry."

"If SEELE knows the security situation here as it stands now I don't think they're going to be too worried about stealth," he countered. "And they probably have enough other ways to get in that would suit that need. Now, assuming they do get into this level, there are a large number of heavy bulkhead doors that separate the blocks...the mechanical level is pretty much laid out like the streets above it. This allows them to drive maintenance vehicles and heavy equipment to where they need it. Unfortunately next to each one is a man sized access door."

She sighed. "So short of welding every single access door in the place shut, which is impossible with the likely time frame we'll have, they are going to gain access anyway."

"True," he agreed. "But getting off that level and into the others is a bit more problematic and we should be able to at least limit them to access points that are the farthest from their objectives."

"Do we know exactly what those objectives are?" she asked.

"Primarily, neutralize the base itself and neutralize the Evangelions," he answered. "If Commander Ikari wasn't lying in his notations or what he told Kaji, we know from the info on the scenario that the mass production Evangelion's role is to essentially capture Unit 01 and use it in the ritual to start Third Impact. Any resistance they encounter, including other Eva units, are to be destroyed. The role of the ground force is to help with that. Capture and or destroy the command centre and its staff and you paralyze the base. Capture or kill the pilots and you neutralize the Evangelions."

"The prime objectives will be the command deck, and the Eva cages, and they will be assuming the pilots will be nearby in order to scramble the Eva's against the attack," she said. "Maybe the hospital too since they would know that's where one of the pilots has been staying."

"If we can direct any invaders coming in through the mechanical level away from those areas by physical barriers, we can at least delay them and maybe force them to come out into areas that we can watch and control most effectively," he concluded.

"We will need to centre our interior defence around the objectives then, but at this point we have no idea how many personnel we can rely on," she said, biting her bottom lip. "The Colonel won't know how many troops he might be able to get to help us out until he speaks with the Secretary General."

"He might be able to pry something out of the Japanese Prime Minister, though I would prefer it if any JSDF help we get was tasked with outside defence," he said. "We don't know how deeply SEELE might have its hooks into their military."

"Sadly the same could be said about any UN troops," she groused. "Even now we still don't know how deep and wide SEELE's influence truly is."

He glanced over at her. "Suppose it's deep and wide enough that they might be capable of dropping an N2 on this place and just crack it wide open instead to get in?"

She just stared at him for a moment before closing her eyes and letting out a groan. "Great, now we need to add aerial cover and a no fly zone to the arrangements. You're such a freaking ray of sunshine sometimes."

"Just being thorough," he grinned as he bumped shoulders with her as he got up. "Speaking of which, I'm going to see if I can find someone from the maintenance staff who knows those levels to go through it with us. Maybe someone who can give us an idea how much surveillance and countermeasures they have in place through the MAGI too."

...Four hours later...

"Ugh!" Lake exclaimed as she flopped gracelessly into a chair alongside the long conference table and rubbed her face with both hands. "If I have to stare at that holo-screen anymore my eyeballs are going to implode."

"At least we made some significant headway," Riker said as she sat down at the end of the table and opened up a gun cleaning kit he had retrieved from his duffle bag in the corner. During the meeting more of their fellow SIS members had arrived from Tokyo 2 and had dropped off the bags with their belongings in them. "Sagawa-san has been here since the construction of the housing blocks and being ex-military himself he had a good eye for this. And Lt. Ibuki was very helpful about what help we can expect out of the MAGI."

"Speaking of her, am I really that scary? she asked. "It was like a good cop, bad cop routine and we weren't even grilling her about anything. Every time I'd ask her something she'd look at you when she answered. When you asked she couldn't answer fast enough...and she'd even smile a little."

"You're a nasty bitch and everyone knows it," he snarked with a grin. "You scare everyone." He ducked an empty water bottle she threw at his head. "She seems a little shy and you were wearing your grumpy face."

"I missed lunch!" she said in her defence.

"So you had to take it out on the poor, cute little computer tech? Shameful. Besides, I can't help it if some people think I'm a big teddy bear."

She snorted. "Got the big and bear part right, but calling you a teddy bear makes it sound like you're soft, fuzzy, and harmless." She pointed her finger at him accusingly. "There is nothing soft, fuzzy or harmless about you mister."

He pulled the pistol under his left arm from its holster, an HK USP Tactical .45, big brother to the 9mm strapped to his right leg, unloaded it, and began to disassemble it. "Your words wound me, oh sour one. Am I not the one upon whom you have fallen asleep countless times when off your ass drunk? Or when flying who knows where on some cold cargo plane to parachute in and bring our special brand of mayhem to some remote corner of the world?"

"That still doesn't make you soft, fuzzy or harmless," she countered, rolling her eyes. "I've seen you essentially take a man apart remember...with your bare hands no less."

He looked her straight in the eyes, intense green meeting shocking blue. "He shot you in the back Mel." That was the only explanation and justification he needed for what he had done to the guy.

"And I appreciate your viciousness in my defence," she said, meaning it. "And I appreciate you carrying me out of there. Even if you didn't tell me you'd been shot too," she grumbled. "Big, stupid bear, you nearly bled to death."

He shrugged. "You would have done the same for me."

She blew out a breath. "Yeah, I would have. Although I hope I never have to haul your ass through a dark, thick German forest for two miles in the middle of the night. You're fucking heavy."

"And you're not?" he smirked.

She gave him the evil eye and the finger. Both of them. He just grinned and continued cleaning his pistol. She leaned her head back over the top of the chair, staring unfocused at the ceiling in silence for a moment.

"So ancient aliens seed the world with life, one of their own gets up to no good, gets sent here for his punishment and rehab, then spends the next several centuries plotting his escape and wants to commit genocide on the entire human race to do it," she summarized. "I mean, how the fuck are you supposed to wrap your head around that and believe it?"

"Even with all of the information we've been presented with it doesn't seem like it should be real," he said. "The sheer scope of everything that has already happened is almost incomprehensible, never mind what's to come. Its like a sci fi horror story come to life."

"I haven't had a decent night's sleep since we got the information from that lecher," she admitted.

"None of us have," he said. She shot him a look. It was the first time she had heard him really admit that this whole thing had him bugged that badly as well. "We deal with the evil and depravity of other people every day to keep other people safe and I believe in what we do," he continued. "But when you find out that some of the most powerful, influential, and supposedly intelligent people in our world have bought in so fully to Kiel's snake oil about forcing mankind's evolution to a higher level, that it will end all suffering and pain, and that they _still_ bought into it knowing that that evolution was essentially oblivion, it leaves any faith you may have had left in mankind in tatters. Then to find out the actual truth behind it all...," his big hands were clenched tightly into fists at this point, even though his voice and the look on his face betrayed none of what he was feeling. "Nothing will ever feel...nothing will ever _be_ the same again."

"I think I'm beginning to understand a little of how Katsuragi must have felt when she witnessed Second Impact," she said, rolling her head to look at him. "There isn't much that really scares me anymore but I don't mind telling you partner, all this shit really scares the fucking hell right out of me."

He set the part he was cleaning down on the table and sat back in the chair, returning her look. "Scares me too Mel. This isn't our usual fare of terrorists or a criminal gang or some shit head that got his hands on a back pack nuke. This is so far beyond any of that. Makes one feel pretty fucking insignificant and practically helpless. I don't like it."

She smiled at him. "That doesn't mean though that we're going to just roll over and die and not kick all kinds of ass."

"A little fear never stopped us before," he said as he went back to his cleaning. "And it isn't going to stop us now. Shit, we have fourteen year old kids here fighting giant monsters with their own giant monsters. If we can't keep fighting with that going on then we might as well drop fucking dead right now."

"With your shield or on it eh?" she smirked.

"Is there another way?" he grinned back.

The door opened suddenly and Lenny rushed into the room. "We've got a problem," he told them.

"What's up?" she asked getting out of her chair as Matt began reassembling his pistol.

"Commander Ikari has disappeared from his office. He was last seen on camera near the First Child's room in the medical wing before the cameras went screwy."

"You two head down there," she said. "I'm going to the command deck and see if they can track him with the MAGI."

Within five minutes Riker and Lenny were exiting the elevator near the nurse's station. No one was at the station at that moment so they proceeded down the hall to the room the First Child was occupying. The door was currently open. They stopped before the doorway and both drew the pistols strapped to their legs. Riker pointed at Lenny and pointed down, then at himself and pointed up, then held up three fingers. Lenny nodded and when the last finger closed into a fist, Lenny went around the doorway in a crouch and Riker stepped around behind him in the high position.

A startled shriek from a young nurse greeted them. She stumbled and fell on her butt, hands held up in front of her.

"Don't shoot me!"

A quick look around the small room told them that she was the only occupant. The bed was empty, the IV needles leaving little bloodstains on the sheets where they had been dropped after being pulled from their patient. Riker holstered his weapon and turned to the nurse. Poor girl still had her hands up and was shaking like a leaf. He squatted down in front of her.

"It's okay," he told her, trying his best, and obviously failing to look non-menacing. "Sorry for frightening you. Are you alright? You didn't get hurt when you fell did you?"

She shook her head. "N-no, I'm f-fine."

He offered his hands and helped her to her feet. "Where is Miss Ayanami?" he asked.

"The Commander t-took her out in a wheelchair," she answered.

"Did anyone try to stop him or ask where he was taking her?"

She shook her head. "No. We were always told that anything the Commander did concerning the First Child was not our business."

"Figured as much," he said.

"This doesn't look promising," Lenny said, directing his attention to the floor near the head of the bed. There was a small drug bottle partially filled with a sickly yellow fluid and a discarded syringe.

"Does that look familiar?" Riker asked the nurse, gesturing to the bottle.

"No," she answered. "There's no label on it so it couldn't have come out of our dispensary."

Riker tapped his earpiece. "You there Mel?" He got no response. "Mel?"

"I thought Dr. Akagi synced our radios up with their internal signal boosters?" Lenny asked.

"She did," Riker answered as he pulled out his cell and speed dialed his partner. "No signal. He must have knocked down the internal wireless comms as well as the cameras." He turned to Lenny. "Bag up that vial and needle, we'll get Dr. Akagi to identify it for us. Never know, it might give us and idea why her took her." He turned to the nurse. "Could you take me to a phone please, I need to contact the command deck."

She led him down the hall to the nurses station and punched in the extension number he needed. On the second ring he got an answer.

"Hyuga," Makoto Hyuga answered at his station on the command bridge.

"This is Capt. Riker, is Capt. Lake on the command deck?"

"She's right here sir."

"Matt?" she answered a moment later.

"Rei Ayanami is missing," he reported. "A nurse down here said Ikari wheeled her out. No one questioned it because apparently you don't question the boss or anything he does in regards to the First Child. We found a suspicious drug vial and used syringe in her room, we're bringing it up for Dr. Akagi to identify."

"Apparently Commander Ikari has a personal override code that lets him blank the surveillance and communications nets," Lake told him. "It's unknown how long the block is set up to last for. It predates Ritsuko's time here so it was most likely installed into the system by her mother. She's trying to crack it now. I sent Gen topside to call Lewis and Fong so they can inform the Colonel when he gets out of his meeting with the Prime Minister."

"We're on our way back up," he said. "Hopefully Dr. Akagi can give us some ideas where we can go looking for him. I seriously doubt he's looking to leave the base."

"I'm rounding up as many people as I can to start looking." She paused for a moment. "Are you thinking what I'm thinking?"

"Yeah," he sighed. "I think that bastard has pulled out one of his back up plans to cause Third Impact."

* * *

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	23. Chapter 23

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

 **Transposed**

 _ **Chapter 23**_

"Damn it!" Ritsuko Akagi swore as she slammed her fist down on the desk in anger and frustration, two emotions that always went hand in hand when dealing with anything relating in any way to her mother. "I know there has to be a way past it but I can't find it! I know she wouldn't have put anything in the system that she couldn't get around no matter what it was or who it was for!"

"I can't bypass it or access the back up system either," Maya spoke up from the console beside her. She was frustrated as well though not nearly as much as her mentor and she did a better job of hiding it. "It's locked out too."

They had been at it for over an hour and couldn't make a dent. After being alerted to the problem they both came to the command deck, Yui coming with them. Capt. Lake had taken over Misato's usual station to utilize the phone to stay in touch with her teams of searchers as they reported in from the handful of locations Ritsuko had given them as possibilities. Colonel McKinnley, Sub Commander Fuyutsuki, and Kaji had just arrived back a few minutes before from their meeting with the Prime Minister. Due to the sensitive nature of what was being discussed, the rest of the bridge personnel had been told to go on an extended break until called for. There was little they could do beyond their normal monitoring work right now anyway and their was precious little time available to explain everything to them.

The door slid open and admitted Matt Riker. "The Dummy Plug lab is a bust too," he announced. "No sign of him having been there either that we can tell."

McKinnley turned to Fuyutsuki. "If he is going to try and initiate Third Impact, does he have what he needs to do it?"

"With Rei he has the flesh of Lilith and with her S2 organ fully functioning he would have a power source to feed the event," Fuyutsuki explained. "But he would still need the flesh of Adam to combine with them to make it happen."

"We took away the sample of Adam that Kaji brought him," Ritsuko said. "The only other source would be from Unit 00 or Unit 02 and we know he can't get to that. He would need access to the flesh beneath the armour or directly into the cores."

"The only other way would be if he had another sample of Adam we didn't know about," Yui speculated. "Since the sample Kaji brought here was the only known one to exist beyond the two Eva's themselves, the only way he could have one is if he cloned another one off of the one we destroyed."

The room went deadly silent for a moment. "That would certainly be within his ability," Fuyutsuki said gravely. "He did most of the work himself on Rei's clones so he could have done it without any assistance from anyone else and it would fit within the numerous contingencies he planned for."

"If he has the means then he could initiate Third Impact at any moment," Kaji concluded, a sick feeling rising in his stomach.

"It shouldn't be immediate," Yui said, clearly running the scenario through her head. "Chances are he would have had to keep a potentially cloned sample frozen after it reached a certain point or he would risk having it grow too much since he had no idea when or if he may ever need it. By what Professor Fuyutsuki and Ritsuko told me the sample that Kaji brought did have a miniature S2 organ but it only really provided enough power to the flesh to keep it alive. Chances are that he wouldn't have let the cloned sample develop one of its own. If he didn't, that means that all of the power to fuel the reaction will have to come from Rei's S2 alone."

"And without Lilith's giant seed body and its residual energies it would take longer for the event to come together and reach a critical point," Fuyutsuki added.

"Why would not having Lilith's seed body make a difference?" Lake asked.

"The parameters of the event require it," Yui answered. "The body must grow to contain the energies that will be building in order to contain and control the event, quite literally to world dwarfing size. That power is needed to touch the souls of every person on Earth, transmute them and collect the souls and transform mankind into one singular entity."

Fuyutsuki continued from there. "Rei's body was originally made from a mix of DNA from Yui and Lilith. Over time her S2 organ, even thought not fully functional, did alter that composition to overwrite the majority of the human DNA element making her for all intents and purposes a direct clone of Lilith herself. However, in the case of initiating Third Impact, there is no substitute for the originals. A clone of Lilith and a clone of Adam's remains will not act and react exactly the same. It will be a longer, slower process especially with Rei's S2 organ being the only source of power."

"Alright," McKinnley said, trying to absorb it all. "But that still means that he could be doing this anywhere. All he needs is time to make it happen without being interrupted."

"And if he does, then how do we stop it?" Riker asked. "Can we stop it if it starts?"

"The only thing that could stop it would be the Lance of Longinus," Ritsuko said. "But we would require an Eva to use it and the only one we even have a viable pilot for is Unit 01."

Maya gasped. "But...that means Ikari-kun..."

"Would have to use the Lance on Rei," Kaji concluded darkly.

"No!" Yui said sharply. "I will not subject him to that. If it comes to that and truly is necessary, then I will pilot the Eva myself."

"Yui..." Fuyutsuki began.

She shook her head. "I don't think he would be able to bring himself to do it and if he did he would never recover from it. I was a part of this madness from the beginning, I already have my share of blood on my hands even if it is from short sighted ignorance and not actual intent or wilful action. He might never forgive me, might even hate me for it and that would crush me, but if it is necessary I will take the responsibility myself."

"Then we'd better make damn sure it doesn't come to that," Riker said seriously.

"I agree partner, but that doesn't narrow down our search for the bastard," Lake said.

"Terminal Dogma!" Ritsuko blurted out. "The room where Lilith's seed body was kept. LCL, Lilith's blood is pretty much the primordial soup that life sprang from and there are thousands upon thousands of gallons of it down there. It still wouldn't be the same as having her seed body to use but it provides a lot of raw material to utilize and might speed things up a bit."

"Do you have schematics for that level?" McKinnley asked urgently.

Ritsuko turned back to her console and in seconds she had a schematic of the Terminal Dogma level up on the large holographic screen.

"There are only two ways in," Fuyutsuki said. "The large doors at the front and a small private elevator hidden at the rear that Gendo has sole control over."

"The main door can only be accessed by four people," Ritsuko said. "Myself, Dr. Ikari, Sub Commander Fuyutsuki, and Gendo. No one, not even him can block access to any of the others short of destroying the door controls."

"He'll probably be armed," Fuyutsuki warned. "And he is a decent shot. It's also possible he may have control over the automated defences down there."

"What kind of defences?" Lake asked.

"Ceiling mounted machine guns," Fuyutsuki answered. "And large directional nozzles to spray Bakelite in case an Eva were to enter without authorization. Weaponry powerful enough to knock down an Eva was not practical down there."

"Any way to interfere with the system?" McKinnley asked.

"I can try," Maya spoke up.

Ritsuko smiled at her. "Have at it Maya. Any way you can find to disable it will be good."

"Right," she said as she got to it, a determined look on her face.

"Even if she can disable the system, I'd rather not have us limited to only one avenue of approach," McKinnley said.

"What's over here?" Riker asked, pointing to an area on the right side of the schematic. "This "L" shaped area?"

"The LCL Plant," Ritsuko answered. "Circulation pumps and filters to keep the LCL usable."

"Can you enlarge that area?" he asked.

"You have an idea?" Lake asked.

"Possibly," he answered. "If this schematic is correct, there is no wall or barrier between the area of the plant and the area where Lilith's body was."

"Correct," Ritsuko said, a slight blush tingeing her cheeks as the large man leaned over her shoulder to look at the image on her screen. "It was always meant to have extremely limited access, as I said before only four people can access that level."

"What about maintenance personnel?" McKinnley asked. "Who looks after the plant if something breaks down?"

"The LCL plant is heavily automated and monitored by the MAGI," Ritsuko explained. "It's a modular design so if something breaks down in any of the modules the MAGI disconnects the entire unit and an automated crane system pulls it out and places it in a freight elevator that brings it to a maintenance shop. A replacement module is then sent back down and put in place. If someone needs to actually go down and look at something or inspect any part of it, that's up to me."

"The bulk of the plant is located in the foot of the "L"," Fuyutsuki said. "In the event that any personnel would actually need to be sent down there to fix anything, they would not even be able to see the area where Lilith was. The work area would be screened off on that side and they would be under close and constant scrutiny of one of the authorized entrants." He sighed. "Thus far that has only been necessary once and unless I'm mistaken Gendo made those people disappear soon afterwards."

"He just becomes a bigger asshole with every story I hear," Lake groused sourly. She turned to her partner. "So, you're going for a swim then?"

He stood up from leaning over Ritsuko's shoulder. "Looking forward to it," he said with a nod. "It's been a while since I got to use any of my UDT skills."

"Yes, because the last time went so well," she snarked, rolling her eyes.

"Hey, we got the job done," he said, unconcerned.

She glared at him. "You were swimming up the intake pipe of a desalinization plant and nearly got cut in half when the impeller blades started!"

He shrugged. "Still here, still in one piece."

"That's enough kiddies," McKinnley chided lightly. "Don't make me send you to your rooms without supper." He usually got a chuckle out of their banter, it reminded him of the time spent with his comrades in the SAS when he was still fully active in the field and before he became involved with the UN. "Lake and I will go in the front door. Dr. Akagi, if you would I need you to go with Matt and take him to the LCL plant. Also, I would like you to be on hand in case Miss Ayanami needs assistance."

"I'd like to go with you," Yui spoke up. "My presence might stay his hand, even if just for a minute or two."

He thought about it for a moment. "Alright, but stick close to us. I wouldn't trust him to be above any action right now, including against you."

* * *

 _ **NERV Hospital**_

While life and death were moving into opposition around him, Shinji continued to drift in the world of much needed sleep. It was just as well really since there was nothing he could do about the situation and he was better off not knowing until it was over. Of course if his father prevailed he would never know anyway, but the unseen visitor to his room would make sure that didn't come to pass.

Mari had arrived back from Russia just after Shinji and his mother returned from Terminal Dogma and she had been watching over him ever since, with the exception of a detour to the command deck to hear what was going on and which she had just returned from. She would need to go and observe what was going to happen in Terminal Dogma and be there in case she needed to stop a potential Third Impact, but she had a few minutes before Yui, Ritsuko, and the SIS people got there. It was a long trip down after all.

She sat on the bed Yui had been occupying and simply watched him. Normally when she visited Shinji she would be following him around and happily talking away to him, commenting on what was going on around him and how he should _really_ react to certain people concerning the things they said and did to him. She would also change the appearance of her attire depending upon where they were, a definite bonus to being what she was and having some power similar to her mentors and overseers. Her school uniform was her default and what she actually physically dressed in, but she could alter her attire at will. It just happened to be a little easier when she was intangible.

Currently she was dressed in a bright pink plug suit, something she really wanted him to see her in since she had seen how he looked at his fellow pilots in theirs. Poor boy always felt guilty about noticing how the skin tight material enhanced the forms of his comrades in arms, always afraid that they would notice and be offended. Mostly that fear stemmed from Asuka's potential reactions. While it was pointless since he couldn't see her, she would still do things that would otherwise tease the boy and leave him with a nosebleed. Like unzipping her plug suit as far as it would go and posing before him, or prancing around him in various forms of sexy underwear. Or even nude for that matter, sharing the bath with him and even laying beside him in his bed and watching him sleep.

She had gained a definite attachment to him and had spent a great deal of time thinking on it. She could feel his soul, his misery and his anguish and loneliness as well as his hidden strength, his caring nature and his desire just to be loved and be important to someone. She realized that these were all things she felt and desired herself, they were very much the same that way. She was grateful to those who found her and saved her, giving her a life and a purpose, but she did not have the kind of closeness and connection to them that she desired.

They certainly treated her well but they were not her family. The closest thing she had to actual family was the man who created her, but she had even less desire to acknowledge that kind of connection to Lorenz Kiel than Shinji now did with Gendo. She supposed that the other survivors of the experiment could be considered her brothers and sisters but there was no relationship there. None of them had ever been awake and aware at the same time, or at least none of the survivors had been. They really all were strangers to one another.

Despite all of the negative things that had befallen him, she had seen Shinji still be able to display kindness and caring to others and had seen the effect it had on him on the few occasions when others returned those feelings to him. She wanted that. She wanted to be able to make him smile and laugh and maybe blush and sputter too and she wanted to feel the kindness and caring he showed. She liked him, liked many of the people around him and she wanted to be a part of that. She wanted to belong. Not being able to actually physically interact with him or them yet was as almost as hard as having to sit back and let events take their course and knowing that harm could come to them all at any moment.

"Even though we both crapped out in the father department, I envy you Shinji," she said as she watched him peacefully sleep. "You have your Mom, Misato, Rei and even Lilith. I don't have anyone that close to me. Gosche is nice, he saved me and has been my mentor for a long time but it isn't the same as what you have with them or even your friends Toji and Kensuke, as dense and dorky as they are. I want to be one of those people close to you Shinji. I may be waaaay older than you, but at the same time I'm no older than you if that makes any sense. I've never done the things people your age always do and I really want to." She sighed as she stood. "I really wanted to stop all of this a long time ago but I wasn't allowed to. I just hope when this is all over that you won't hate me because I had to stand back and let things happen."

She took a moment to compose herself before disappearing and heading for Terminal Dogma.

* * *

 _ **With Gendo**_

The ride down to Terminal Dogma gave Gendo time to reflect one last time on what he was doing. He was rather angry with himself over all the vacillating he had engaged in since Yui's return. From the moment he had learned of it, his goal had always been to enact Instrumentality. While her loss to the Eva had prompted him to hijack the thing toward his own personalized scenario, the desired overall end result had always been otherwise the same and he should not have lost sight of that just because she had returned. Even if she had fallen lovingly into his arms upon her return his aims would have remained the same and he would have continued onward with the scenario that he had devoted so many years and all of his time and energies to.

He regarded the world as a cold and uncomfortable place, a place unfit for living in. The pain in its various forms that living was, the miseries that people inflicted upon one another were like dark shadows that constantly clawed away at one's sanity. Bouts of peace and happiness were fleeting and brief, never lasting more than the blink of an eye compared to the misery. Without a doubt he knew that he had added to his own misery and pain during his youth but he was only laying structure on top of the foundation he had been given by his own family.

He had also learned how to use the lessons taught to him by his pain and misery to manipulate others to his whims. He was intelligent, his grades right up and through university confirmed that, but he was also sly and a schemer. He developed a force of personality that allowed him to bend people to his will to get what he wanted from them. He had no compunction or remorse at all about his manipulations. He would use them until there was nothing of value left in them and then throw them away like they were nothing. Once they were gone it was like they never existed in the first place. Even his own son was not exempt. He was nothing to him but a means to an end.

Not even Yui had been exempt as she turned out to be the one speck of light in a sea of dark. She was the only person who had even given him a chance and believed in him. But even the love he grew to have for her was not enough to turn him onto a different path. Rather than let her love alter his direction, he pulled her down the dark path with him. He was too far gone to have ever moved in that other direction anyway, his desire and need to put an end to mankind's suffering, _his_ suffering because that was all that truly mattered, was unbreakable.

While he had examined the idea of Yui somehow returning from the Eva, it had been such a remote possibility that he had buried it at the bottom of the pile of all other possible variations to the scenario that he had charted and accounted for. Losing her to the beast had driven him even harder. He had lost the only thing that had ever been good in his life and while he had always been committed to Instrumentality, losing her had turned it into a obsession and an intense desire to take control from the old men and enact his own version just for the chance to reunite with her in oblivion.

By the time she did indeed return any such possibility had been long purged from his mind and thus he was unprepared when the impossible did indeed come to pass. He wavered and stumbled and began the process to give up Instrumentality by giving the information to Kaji. Even as it became clear that Yui had changed her mind about it and was beyond angry with him over what he had done to her son he still wavered. He still thought that even if she despised him, having her back among the living was enough.

But, it was not. It never was and it never would be. Nothing but the end would suffice no matter what and he had monetarily lost sight of that. Fortunately he had accounted for the possibility of being found out, even if he had never envisioned that the rat would in fact be himself. He had never counted on his own resolve ever wavering but it didn't matter, he had contingencies available that could be adjusted to work and get his desired result.

He looked down to his left where Rei sat slumped and strapped into a wheelchair, looking very much like a marionette with its strings cut. Her eyelids were partially open, just enough to tell that her eyes were rolled back. The drug he had given her was designed to immobilize her, the effect was like having all ones tendons and ligaments cut. She couldn't move and would have slid out of the chair in a boneless heap if she wasn't restrained. Even if she could move she would offer no resistance. The drug had a strong narcotic effect that essentially left her as stoned as a bus full of hippies and she would be so disoriented that she wouldn't be able to form coherent thoughts.

He felt even less for her than he did for his son. She had been designed for a specific purpose and no matter how she felt about it now she was destined to play whatever role he demanded of her. Her life had never been her own, it was his to direct and either prolong or end as he saw fit just as he had with her first incarnation. No matter what she was a slave to his purpose and that purpose was crystal clear to him once again. There would be no more wavering, no more second thoughts or reflective angst. Even though it was through an alternate scenario the end was still about to come. The only regret he had was that he would not get to see the look on Kiel's face when he realized that he was not going to be able to escape his sentence, that the payoff of his plan that had been centuries in the making was going to slip through his decrepit and withered old hands.

When the elevator reached its destination and the doors opened, he slung the large metal case that was resting on the floor next to him over his right shoulder by its carrying strap and wheeled Rei out. A short trip down a dark corridor brought them out into the light near the now empty cross that once held Lilith's body. He paid it no mind as he moved up the side of the LCL pool until he was perhaps three quarters of the way up its length. Before locking out the communications system he had prepared everything he needed. He programmed the automated defence system to react to anything that moved beyond the edge of the LCL pool at the point closest to the entrance to the room. There was no need to cover his back since he was the only one who could gain entrance via the private elevator.

Even if someone were to be able to break into the elevator shaft and make their way down, there was a thick bulkhead door on the level above that closed off the bottom of the shaft. It would open to let the elevator car pass then close up again immediately after it did. As an added precaution just in case, the roof of the elevator car was made of six inches of steel plate and there was no access hatch in it. Any visitors he had, and he was sure that they would eventually figure out where he was, would have to come through the door before him.

He set the case down and undid the straps keeping Rei in the wheelchair, roughly holding her up by a fistful of her hair as he shoved the chair back and away. Laying her on the floor he reached into the right hand pocket of his uniform coat and withdrew a folding knife which he failed to thumb open with his bandaged hand. A week after the surgery to remove the fragment of Adam from it and he still couldn't fully use it. Switching it to his left he opened it and proceeded to cut off Rei's hospital pyjamas and underwear, not caring if he cut her in the process. Pulling away the now ruined clothing he tossed the rags in the direction of the wheelchair, leaving her lying naked on the cold concrete floor.

Putting the knife away he turned to the large case, tipping it down to lay flat on the floor and kneeling before it. He opened a hatch in the middle of the lid and began punching in numbers on a keypad. The small display lit up and prompted him to enter what turned out to be a rather long password, then a second one as an added fail safe. Once the second one was entered there was a series of whirs and clicks to be heard coming from within the case. After a minute of this he was prompted for a third and final password. As it was accepted there was a hissing sound as four vents opened, one on each end of the lid, two at the back of the bottom half of the case. A few seconds later cold, white vapour began to drift from the vents on the base.

The thawing process for the contents of the case would take several minutes to complete. He retrieved the wheelchair and placed it where he had been kneeling and sat down. Might as well make use of it while he was waiting. Reaching into the left pocket of his uniform coat he pulled out a silver Sig Sauer P229 pistol and held it in his lap. From the inside left breast pocket of the coat he pulled out a small remote control device and settled in to wait for his inevitable visitors.

He didn't have long to wait. In less than ten minutes the massive doors opened and admitted Yui, the SIS commander, and the woman that had punched him and knocked out one of his teeth.

"That's far enough," he told them as they reached the end of the LCL pool, his point accentuated by the whirring of the automated guns coming on target. "Advance any further and the guns will open fire." He held up the remote in his right hand. "If I activate this they will fire on anything that moves between my position and the doors."

"I'd like to say I'm surprised by this Gendo," Yui spoke. "But we both know that this was always your aim, with or without me here."

"You are correct," he said, getting to his feet. "There was never any other option."

"You despise humanity that much?" Lake questioned bitterly.

"Why shouldn't I?" he responded. "You of all people have seen first hand the worst depravities and malice that humankind practices against itself."

"Yes I have," she said. "I have seen horrible things that I can never forget no matter how much I wish I could. Those things have scarred me for life but that doesn't mean I want to put an end to the human race."

"You believe that you are making a difference by ridding the world of its worst elements, but where is the proof of your progress?" he asked. "You can't show such a thing because there is none. For every predator and sick ideologue you remove from society, more take their place. It is a hydra that you cannot hope to defeat Captain. You are fighting a losing battle."

"Maybe so," she admitted. "But you're not telling me anything that I don't already know. I'm not naive to the ways of the world and I fully realize that what I, what _we_ do may be futile. But that's not going to stop me from doing it. We do what we can and we do it because someone has to."

"You claim not to be naive yet you live your life engaged in useless altruism," he smirked drawing her ire. "A fascinating dichotomy if there ever was one. I have no such illusions. While the old men under Kiel's thumb believe that everything they have done is because mankind has ceased to evolve and needs a push, I have never once considered such nonsense. However I also do not believe that there is anything within mankind that is worth saving."

"The technologies we have developed since the inception of Project E could do so much good for the world," Yui said. "Yes, the world is a mess and mankind preys upon itself, but the discoveries we have made could do so much to change things. We could kick start the process to make real and meaningful changes. A lot of good can still be done."

"But it won't be," Gendo countered. "After the devastation of Second Impact mankind had the opportunity to come together for its common good and survival yet it chose to go to war against itself yet again instead. As I'm sure the Colonel could tell you since he has the ear of the Secretary General, there is great discomfort among many of the UN members over what will happen with the Evangelions upon the defeat of the Angels. What do you think is likely to happen then? Mankind's evolution may not be at a dead end, but it has become stagnant and slow. Despite our advances we still cannot move beyond killing each other for any number of untold reasons, victimizing each other at every turn. It breeds upon itself making life that much more dangerous and unbearable every day."

"And you made things a thousand times worse when you helped initiate Second Impact," Lake growled angrily. "All because you were pissed at how you saw the world treating you. You selfish, sick bastard!"

"Perhaps I am," Gendo said as the case at his feet beeped and the latches keeping it closed released and opened. "And I can admit to my weaknesses, but that is not going to change the end result. This is what I have worked for since the moment I first learned of the Human Instrumentality Project and now I have the added bonus of denying that old fossil Kiel in getting what he wants."

He knelt down in front of the case, laying his pistol on the floor and transferring the remote to his left hand. This was it, the moment was finally at hand. While it wasn't how he had foreseen it happening it was still an acceptable method. So long as it happened and was guided by his actions that was all that mattered. That was why he had painstakingly planned for so many contingencies in his scenario, doing everything he possibly could to make the chances of its success as close to a certainty as it could be.

As he opened the lid of the case he heard the dying whir of servo motors and looked up to see the automated defence guns sagging in their mounts. The thought passed through his mind that given her absence it was probably Akagi who had found a way to bypass his control and disable them. He wasted no time in grabbing the mass of flesh that was the cloned remains of the First Angel and turning towards Rei's prone body. He saw the two SIS members reaching for their guns and beginning to move toward him. He knew they would never reach him or get a shot off in time.

Out of the corner of his eye he saw something in the LCL pool. In the brief flash of milliseconds he recognized the large form of the female SIS Captain's partner rising out of the orange liquid. He registered the sight of the breather mask covering his face and realized that he had actually overlooked something, that he had left one tiny little flaw unchecked. While he was certainly cognizant of the fact that any of the other three people who could gain access to this level could and probably would bring help with them if they figured out where he was likely to be in time, he had overlooked the possibility of someone approaching him by swimming through the LCL reservoir. A bitter reminder right at the most crucial moment that nothing and no one, not even him, was perfect and could account for every possibility. He too was fallible.

The other thing that registered in his sight in that instant was the large calibre pistol, enclosed in a clear plastic bag to keep it dry, that was filling the man's right hand. He saw the flash but never heard the sound or felt the impact as the bullet smashed through the orange tinted lens covering his left eye, cored through his brain, and blew out the back of his head. Gendo Ikari, the Bastard King of NERV, gracelessly flopped over dead next to Rei's prone form, the misshapen glob of cloned flesh that represented Adam spilling from his hand and onto the floor beside him.

By the time Riker, wearing nothing but his boxers, a belt holding a small air bottle, and the breather mask attached to it climbed out of the LCL, his partner and the Colonel had secured the body and removed Gendo's gun and the remote from his vicinity. While it was obvious that he was dead and a check of his pulse had confirmed it, it was standard and habitual practice that only a fool would fail to follow.

As he removed the mask and the belt Dr. Akagi entered the room carrying a large black equipment bag and hurried over to them.

"I could use your help for a moment Yui," she said.

She set the bag down and opened it, removing a large, cylindrical metal container about the size of the average fire extinguisher and standing it next to the bag. Next she pulled out two pairs of heavy, thick gloves and a long set of tongs. She handed a pair of gloves and the tongs to Yui.

"As soon as I open the container drop the sample of Adam into it," she instructed.

She put her own gloves on and released the clasps sealing the cylinder. As soon as she opened it white vapour began to flow from it as the room temperature air met the liquid nitrogen inside causing it to boil. Yui picked up the harmless looking blob of pale flesh and placed it inside the cylinder. Ritsuko immediately closed it and refastened the clasps, breathing a sigh of relief when they clicked into place.

"Dr. Akagi," Riker called, getting her attention. "Ayanami isn't doing so well."

She turned to see him checking the pale girl's pulse. She was breathing heavily, shaking and sweating. "Damn it," she swore, coming to the girl's side and drawing a syringe and vial of clear fluid from the pocket of her lab coat. "He must have given her a little too much. That stuff isn't easy to dose on the fly like that." She knew, because she had been the one to create it at Gendo's order and the people standing around her knew it. They didn't say anything because they had seen the guilt she felt when she told them about it earlier in the day. She was grateful for their silence.

"Will that offset the effects?" Yui asked as the other woman stuck the syringe in the vial and drew the fluid into it.

"Not completely," Ritsuko answered tightly. "It should keep her from overdosing and it should at least restore her motor functions but it likely won't restart her S2 or greatly reduce the narcotic effect. She'll have to ride that out unfortunately."

"I can kick start her S2," Yui said as she knelt next to the girl and Ritsuko gave her the injection. "I have something I need to give back to her anyway."

Just as she had when she borrowed a bit of her soul's energy, Yui placed one hand over Rei's abdomen where her S2 organ would be and the other over her heart. Her hands began to glow as she returned what she had borrowed, with interest. Lilith had told her how much more she could safely give the girl and it would take some of the burden off of herself with the extra bit of Lilith's soul she had acquired the last time she was in Terminal Dogma.

"Sorry it took me so long to return this to you Ayanami-chan."

* * *

 _ **Rei's Inner World**_

She had been about to awaken after her long, largely enforced sleep. She could hear the sounds of the machines in her hospital room becoming clearer to her hearing and her eyelids were fluttering, gradually letting the dim light into her vision. As her eyes began to open further she felt a presence next to her. When they opened fully for the first time in over a week she saw Commander Ikari staring down at her coldly and she felt a needle pierce her neck. Fear washed over her as her eyes rolled back in her head and her body began to feel numb. The freedom she had begun to anticipate and long for was about to be taken away from her. She was becoming his puppet once again.

She crashed into her inner sanctuary with a splash. She thrashed and sputtered as she surfaced, her drug addled mind unable to tell that this was her inner world where she could never drown and not some body of water in the outside world. She couldn't stand, she stumbled and staggered, falling back under the water only to resurface and repeat her uncoordinated actions. The world spun around her wildly as she flailed and floundered, her mind filling with panic as she tried desperately to stay upright, to make the spinning stop. She cried and sobbed and whimpered in terror. Everything she had discovered that she truly wanted, to be away from her given purpose, to have a life to call her own. Shinji. It was all being taken away from her and she couldn't do anything to stop it. Her mind and body would not answer her commands. The Commander was going to get his way. He was going to destroy everything and use her to do it even though she no longer wanted any part of his plans, no longer wanted anything to do with him.

After a long, agonizing while her body began to slow down, to feel sluggish. She fell back down into the water and floated limply. She began to shake, her breathing quickened, and she felt like her body was burning up. Her thoughts all seemed to run together and become a jumbled, unrecognizable mess, little more than screaming white noise that clawed at her sanity. When it finally, mercifully ceased the abrupt silence was almost as maddening. She could begin to feel her body again but her senses and perception still seemed muddled and confused. A bright light began to overwhelm her vision and her body began to tingle, almost like there was a mild current of electricity running through the water.

Suddenly she bolted into an upright sitting position. She was no longer in the water but sitting on a cold, hard surface in a totally different environment. It took her a moment to realize that she was now surrounded by people, five of them. It took a moment again to recognize Shinji's mother and Dr. Akagi, but she didn't know the other three. There was a man in a dark suit, a woman in a t-shirt and dark pants...and a man wearing nothing but a pair of boxer shorts. They were wet and clung to him like he had just gotten out of the water. Several seconds later she clued in that she was next to the LCL pool in Terminal Dogma.

Terminal Dogma...funny name. Why was it 'terminal' and why Dogma and not...Catma, or...She nearly giggled before her brain got back onto the tracks...somewhat, and turned her attention back to the man in the shorts. She seemed to move in slow motion as she looked up, and up...and stopped partway, coincidentally enough the level of his saturated and clingy boxers...then up and up until she met a face with a slight, amused smile and a pair of green eyes. She looked at him for a long moment.

"You...are very large," she slurred.

"I suppose I am," he grinned.

Her eyes travelled back down, stopped, then travelled the rest of the way down. She looked down at herself, then slowly up at the woman she didn't know. She went to speak, but stopped and looked back down at herself, her chest in particular then back at the woman as if she was making a comparison. Her eyes seemed to lose focus and she wobbled a bit.

"I am naked," she said simply. She looked down at her chest again. "And small."

It was all that everyone could do not to snicker out loud. "You are also very stoned my dear," Yui said, unable to keep a smile off of her face despite all that had transpired.

"Shinji-kun has seen me naked," she said, nonplussed. She smiled. "Twice."

"Okay little Miss Exhibitionist," Ritsuko said with a slight grin as she wrapped her lab coat around Rei. "We need to get you up to the hospital and check you over, get some fluids into you and let you sleep this off."

Her cell phone suddenly rang and she retrieved it from the coat pocket. She smiled when she saw who was calling. "Hello Maya," she answered.

"Sempai! Are you alright...is everyone okay? I got the auto defences to shut down...I just hope I was in time."

"Relax Maya, you did great," she answered. "Your timing couldn't have been better actually. The threat is over. We're about to bring Rei up to the hospital. The drug has her kind of loopy but she'll be fine."

"That's good." The relief was evident in the little tech's voice. "The comm system just restarted by the way, as soon as it hit the three hour mark since the Commander shut it out, it rebooted."

"Hopefully we can try back tracking it and take another stab at finding that program," she mused. "I'll see you when we get back up."

Colonel McKinnley retrieved the wheelchair and helped Ritsuko get Rei into it. By this point the girl had gone quiet and had a silly little grin on her face to go with her unfocused eyes. He was pretty sure that he heard her mutter something about 'Shinji-kun', and 'naked'. He turned his attention to Ritsuko and Yui.

"Mel and I will escort you topside," he said. He looked to Matt. "Sorry, but you get body detail. We'll be back as soon as we can to pick him up."

"It'll give me a chance to dry out a little," he said, snapping the waistband on his shorts.

As they walked off and he gave his partner the finger for the smirk she gave him, he swapped his pistol for Gendo's, checking to make sure it was in working order. His pistol had been dunked in the LCL after he took the shot. He'd had no way of knowing that the defence guns had already been disabled so he wasn't about to leave himself exposed any more than necessary. The LCL might not have done much to slow the bullets until he got near the bottom of the pool, but it was better than nothing. There was also some melted plastic from the bag at the muzzle which was another reason not to fire it if he had another option.

He looked down at the body of Gendo Ikari. No doubt the man was dead but they weren't about to leave the body unattended, even if there were supposedly only four people, three now, who could access this level. They had already removed a lot of rats from the place and he had no doubt there were more around still that answered to SEELE. They were leaving nothing to chance. Besides, it was pretty much procedural.

"That's one major bastard down," he said aloud. "You're next Kiel. We aren't going to let you succeed either."

The girl in the pink plug suit watching him from atop Lilith's cross couldn't have agreed more.

* * *

Finally, Gendo's dead. Rot in pieces you bastard.

For those questioning why Capt. Riker was wearing a breather when he swam through the LCL, remember that you can't breathe the LCL unless it is electrolyzed, and the LCL in that reservoir would not be. Without the breather it would be just like trying to breath any other liquid. You'd drown.

Please leave a review if you would be so kind.

And while you're here, check out my other stories.


	24. Chapter 24

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

 **Transposed**

 _ **Chapter 24**_

 _ **Three Days Later**_

 _'I'm still not entirely sure how I should really feel,'_ Shinji thought as he walked Unit 01 through the countryside and off towards were Lilith was leading him. The Lance of Longinus was gripped in the Eva's right hand and he was off to slay the Sixteenth Angel, hopefully before it hatched out of its chrysalis and became dangerous. He had just passed by the area where the cemetery was located that they had buried his father in the day before and it reignited his uncertainty.

While his feelings weren't as jumbled about it as they had been three days ago he still felt odd about the whole thing. His father had done so many bad things, hurt so many and had tried to end the world. Yet he found that he couldn't bring himself to not feel something at his passing. He had been even more puzzled when Captain Riker had come to him and his mother, bowed, and apologized for what he had needed to do to stop him. Shinji had understood that well enough, but he was puzzled why the man would feel it necessary to apologize. He had stopped his father from ending the world after all.

" _He may have done horrible things,"_ Riker had said. _"But he was still your father and your Mother's husband, someone who at some point you both did love."_

He and his mother had talked for a long time after that about it. Even though they had both come to despise him, before that Gendo had been someone they both had a deep attachment to and it was that part of themselves that felt the loss, the part of them that remembered a better time with him even if it was brief. He knew that his father had never really had a deep attachment or love for him, but he had had the love of a son for his father, a love born of being too young to have known what kind of a man he really was. All he had known was that he was one of the two most important people in his life.

He could never forgive him for what he had done to him, to so many other people. He could never forgive him for the atrocities that he had been a part of and for the one he had still been trying to enact right up until the end. But he had still been his father and it would take a while to deal with this.

' _Just remember that you're not alone Shinji,'_ Misato's voice whispered in his mind. _'You have us and your Mom and Rei.'_

' _I know and I'm grateful,'_ he sent back. _'I'm kind of worried about Rei though. She hasn't said much.'_

' _I have been talking to her,' Lilith_ said. _'As you know it is difficult for her to understand and communicate what she feels. Until she discovered feelings for you, Gendo had been everything in her world and even though she now realizes how heinous he was, she is confused just as you have been. Simply be there for her and when she is ready then maybe she will speak to you of it.'_

' _Until then, we've got an Angel to ambush,'_ Misato reminded them. _'I just hope this goes better than the one in the volcano did.'_

 _'Even if it does emerge it should be disoriented with no 'call' to direct it,'_ Lilith explained. _'And it will be no match for the Lance either way.'_

She was correct. When she tracked its location to a spot several miles outside the city and leading up into the foothills, they arrived to find a worm like mass of flesh thrashing about and trying to escape its chrysalis. A stab of the Lance and it exploded into a splash of LCL.

"I wish they had all been that easy," Shinji muttered.

* * *

 _ **Back At NERV**_

As was usual in Ritsuko Akagi's life, work always seemed to be piled up waiting for her attention. She had the tests that she had thus far been able to run on Yui to finish analyzing, but since the woman seemed fine they had to take a backseat to getting back on track with the project to further protect the MAGI and back hack its expected attackers. Fuyutsuki and Yui told her they could handle over watch on Unit-01's sortie to find the Sixteenth and that they would call her if they needed her expertise, thus freeing up both her and Maya to get caught up on their programming. However, she wasn't getting much done.

"Sempai?" Maya called for the third time, finally getting her attention.

"I'm sorry Maya, what is it?" she asked, rubbing her eyes.

"Are you alright?"

She sighed. "I guess there's no point in me saying that I am is there?"

"Sorry," Maya apologized. "I don't mean to pry."

"You're not," Ritsuko assured her. She was glad that someone actually cared about how she was doing.

"Is it...about Commander Ikari?" Maya asked meekly.

Ritsuko leaned back in her chair and let out a long breath. "I suppose you could say that but not so much in regards to the personal relationship I had with him. Frankly, I've become jaded enough that I can say I'm glad that he's gone even though I'm just as responsible for letting myself be used as he was for using me. I was already hurt badly enough by my relationship with him to be hurt any further by his death. This has more to do with realizing the cost and the risks others are having to take to undo what I helped to put in place." She smirked. "It's things like this that make me sometimes wish I had never rediscovered my conscience, but then I'd probably be as dead as he is."

"What is it that got you thinking about that?" Maya asked.

"I had a conversation with Capt. Riker when I showed him into the LCL plant."

* * *

 _ **Three Days Earlier**_

A swipe of her card let them through the main door into the LCL plant. It was a mass of pipes and tubes, pumps and filter pods and it was massive. A short trip down a narrow alleyway led them to another smaller door which also yielded to her card. The room was roughly fifteen by fifteen feet and sparsely outfitted. There was a bench and a locker along one side, and a set of shelves on the other that contained breather masks wrapped in clear plastic bags and small air bottles that were good for about fifteen minutes of use. There were also a couple of pairs of swim fins, a pair of underwater lights and a couple of magnetic hand clamps. There was another door on the opposite side of the room.

"That door will take you out to a gantry that connects to the main intake module," she explained. "But just outside the door is a ladder down into the LCL. That's where I go in if I have to go inspect something."

"Thanks Dr. Akagi," he said as he looked over the breather masks and air bottles. "And these will do the job nicely." He grabbed one of each and set them on the bench then began removing both his leg and shoulder holsters. "Been a while since I went swimming on a job."

"Aren't you worried about this?" she asked. "If he has control of the auto defence guns they could turn on you the moment you break the surface."

"Well," he began as he sat down and took the breather mask out of its bag. "I have to assume that he does indeed have control but that doesn't change anything." He put his .45 in the bag, knotted it closed and checked to make sure he had enough play in the bag to get his finger in the trigger guard without puncturing the plastic. "We need to come at him from more than one side and this is the only option we have to do that."

"They're armed with machine guns and they come on target quickly," she said. "You won't have anything to use as cover...they would tear you to pieces."

He shrugged as he began undoing his boots. "Occupational hazard," he answered. "One bullet or a hundred, I could be dead either way. If those guns turn my way I'll have time for one shot but that's all I'll need. One shot and go back under. If I miss it likely won't matter if the guns turn on me or not." He pulled off his boots and socks, then pulled off his shirt. "Sorry, I know undressing in front of you is probably pretty rude, but under the circumstances..." He shrugged again.

She wasn't minding the sight, not one bit, and to hell with manners and propriety, that wasn't the issue. He just seemed so...unperturbed by the idea that he could be swimming into a lead buzz saw if those guns turned his way. She knew he was a soldier, she could see the evidence of past actions in the scars that she could see upon him. But he looked and acted like he was just off to take a leisurely swim in the pool and not swim potentially right into the sights of several machine guns in order to prevent the end of the world. Damn it, she was so nervous she was about ready to piss herself.

"How can you be so nonchalant about it?"

"It's what I do," he said simply. "I put myself in the way of extreme harm every day so that others don't have to and so that I can undo the schemes of people like Gendo Ikari and Lorenz Kiel. Doing that and watching my partner's back are the most important things to me and I know the price I could pay for it." He removed his pants and set them aside, leaving himself clad in just his boxers. "Believe me, I'm not as calm as I probably look on the outside but it's alright. That bit of fear keeps you sharp and laughing at it keeps you sane. While the Colonel and my partner keep Gendo distracted I'm going to come up on his blind side. If I miss and the guns turn on me then I become a distraction for them to take advantage of and succeed where I might fail."

"Even if it gets you killed?"

"Even if it gets me killed," he echoed. "If Gendo succeeds, _everybody_ dies. I made peace a long time ago with the price I might one day pay to undo the bad deeds of others, but that doesn't mean I'm eager to pay that bill any time soon. I plan on defying the odds for a long time to come." He smirked. "It runs in my family. Most of us have served in the military for generations and we have a habit of having long careers." He stood and fastened the belt for the small air bottle around his waist.

"Then I suppose I should say thank you for what you do then Captain," she said sombrely. "Especially since I had such a hand in helping Gendo's plans along."

"I know the story and I know a victim when I see one," he said evenly. "And I know that you're smart enough to realize how things would probably have gone already if you were still helping him." She nodded her head in understanding. "But you aren't and I can see the remorse you have and I see you trying to stop it all. That's all I need to see and know." He smiled. "And you're welcome by the way."

She picked up the breather mask and connected it to the air bottle for him. "I guess all I can say then is good luck."

He picked up his bagged pistol and shoved it into the waistband of his shorts at his back. "I'll take all of it I can get."

She unlocked and opened the door to the gantry as he turned on the air bottle and checked the flow into the mask. Satisfied he turned it off so as not to waste it. He stepped out onto the gantry and began his decent down the ladder, stopping to look up at her once he was waist deep.

"Despite all of the dangerous possibilities, do you know what's going through my mind right now?" he asked with a smirk.

"Dare I ask?" she said, raising an eyebrow.

"I was thinking that I should leave the shorts behind and show up buck naked," he grinned. "It would drive Mel nuts. She'd yell at me for an hour and call me things you've never heard of before. Probably ask me if I felt the need to give you a strip show before I showed up. At least it would make us forget for a while how freaking scary all this end of the world shit is."

She couldn't help but grin. "Maybe I should tell her you did just to see what happens."

He laughed as he turned the air bottle back on and affixed the mask to his face. "I like you Doc. See you on the other side." He winked then disappeared beneath the surface and was gone.

She sighed. "I'd better see you on the other side Captain. On the other side of the reservoir and not wherever we end up if Gendo succeeds. And you had better be alive and well and in one piece."

* * *

 _ **The Present**_

She looked Maya in the eyes when she finished the story. "It made me think about what others have gone through to try and stop what I had such a large part in trying to bring about. I knew that there were people that were trying to find out what NERV and SEELE were doing behind all of the secrecy, and that there were people who had reason to be suspicious. I knew what the end game was so I didn't care how many died while trying to shine the light of day on us. I was too interested in trying get a man who only saw me as a tool to love me to ever even think about it."

"But that's not who you are really are Sempai," Maya assured her. "If it was you wouldn't be doing any of this." She gestured to the computers and manuals and books of notes they had accumulated for this project. "You wouldn't be trying to stop what's happening."

"There is no guarantee that I would be trying to stop them if Dr. Ikari hadn't come out of the Eva when she did and got me involved," Ritsuko said. "Even though I was finally realizing exactly what I was to the Commander, that in itself wouldn't have been enough. I would have just kept doing what I was doing because I would have felt there was no point in doing anything else. He broke me Maya and I would have continued on just to finally have the pain and the hurt stop when he reached his goal."

"I don't believe that," Maya said, taking Ritsuko's hands in hers. "Because I see evidence to the contrary sitting right in front of me. I know you're still hurt but you're fighting back."

"But I'm not doing it for me Maya," she said, all but crying now. "I'm a lost cause and I don't think I can say that I'm doing it for the rest of the world."

Maya shot out of her chair, a hand going to either side of Ritsuko's face and she leaned in closer. She seemed almost angry. "Don't say that Sempai!" she all but yelled. "You are not a lost cause. You're out from under his thumb and you were given a second chance and you've taken it." She lowered her voice. "And you're not alone, I'm here and I won't abandon you. I want to help fix what he broke."

She brought her hands up to cover Maya's. "Do you know what you're implying, what you're asking?"

"I...I do," Maya said quietly. "I just want you to be happy and live your life how you want to Sempai, without someone else trying to control you and make you miserable. "I want you to be free. I want to help you get there."

She couldn't help it, she wrapped her arms around the girl and pulled her tightly to her. "I don't deserve someone like you Maya, I truly don't. But I'm so glad that you're here. I'm so glad that you care and that you believe in me and _you_ are what's keeping me going. You're the reason I'm doing this, the reason why I even want to try."

She leaned forward into Maya a little more and it proved to be a little too far. Her rolling chair shot out from under her and pitched them both to the floor with matching little shrieks of surprise. There was a moment of silence followed by a snicker, then full blown laughter.

And neither let go of the other.

* * *

 _ **Pilot's Locker Room, A Few Hours Later**_

Rei stood naked before her locker, staring blankly at both it's contents and the plug suit she held in her hands. All things change but to someone like herself who had lived such a structured and rigidly controlled life, even small change represented major upheaval for her. Large changes were almost cataclysmic and she had been experiencing change on both levels lately.

The large changes had of course begun with the return of Dr. Ikari and the end of the purpose she had been created for. It had left her feeling so lost because she no longer had a purpose or a sense of direction since Commander Ikari had not contacted her after the incident. Having no direction and no idea what she was supposed to do had been horrific. So had the belief that she was likely to be put down like an unwanted stray and just as she had been realizing that she didn't want her end to come. She did not want to die and it had been her interactions with Shinji that had made her realize it. She had been so lost and so distressed in her turmoil that she had allowed Soryu to nearly beat her to death in a bout of madness.

The next frightening change dealt with Shinji learning the truth about her and she discovering the true nature of her feelings about him. If it hadn't been for Lilith's intervention she was positive that she would have mentally collapsed in upon herself and never recovered. Due to her upbringing and conditioning it was very hard for her to identify and quantify her feelings and emotions. She had trouble connecting the dots on why certain actions and events made her feel the things she did. She simply didn't understand, she had no knowledge or experience to draw from. Such things had always been deemed as unimportant so the dynamics of it had never mattered.

She was feeling that disconnection again now in regards to Commander Ikari's death. He had been everything to her. While she hadn't realized until recently that that had not been a good thing, he had been the very foundation upon which she lived and she had been happy to fulfill her role in his plans. He created her, gave her a purpose for her life which was something most people never found. She had been content at his side and content to play her role. She did not need a sense of individuality or to be socially active and accepted. They were distractions, things that could make her stray from her purpose and the purpose she had been given was everything.

But that was wrong. She had been conditioned, programmed like a lifeless computer to carry out every daily task in a certain way. It robbed her of even the ability to know that she had no choice about anything in her life. But it took so little to put cracks in that false facade and make her begin to see that there was something, something more than her purpose and it was not unimportant or pointless. Shinji had made it possible for her to see this, to begin to see beyond her programming and see that there was a world beyond it for her.

But it was so hard. The regimented structure that her life had been made things easy. She didn't have to feel anything or care about anything but her given purpose. Dealing with her feelings and emotions in the absence of that purpose and regimentation and the lessened mind numbing effects of her medications was hard, it hurt, and the growing influx of new and unknown feelings and emotions was difficult to handle. The prospect of now living outside that box the Commander had put her in was terrifying yet she didn't want to go back to it. Commander Ikari had been wrong about so many things and that realization had been quite the revelation for her. So many of the things that he told her were useless and of no consequence, were not. It would be difficult for her to adapt to a new way of living but she wanted to and she would have Shinji to help her do it.

But Commander Ikari had nearly taken that all away from her just as she had only began to discover what she wanted for herself. It had been terrible when she realized what he was doing and she finally saw him for what he really was. She had wanted to run but the drug had immobilized her so quickly she couldn't do anything except see her hopes crushed and fall into a nightmare. Luckily she awoke from that nightmare but the memory of the terror she felt had lingered and made her recovery from the drug that much more miserable. She had begun to feel better when they allowed Shinji to visit her.

She didn't know why but when she was near him she always felt warmer, felt like...she belonged? She didn't know how to quantify it. She just knew that she felt better, happier around Shinji. He would not hurt her, would not use her. He was the new anchor and light in her life. But if that was so, then why did she feel so conflicted and out of sorts about Commander Ikari's death?

Everything had always been black and white to her. If anyone else had done what he had been attempting and was stopped, killed as he was, she would have seen it as a necessary and acceptable way to prevent such a disaster and would have felt no remorse for them. So why could she not feel the same in regards to the Commander? Lilith had said that because the Commander had been such a dominating presence in her life, because he had created her and shaped her and made her to be so attached to him, that it was not strange that she would have mixed or conflicted feelings. She could understand that point but it was the emotional responses she was having that were making it such an issue and ordeal. The two things seemed to be at odds with each other.

' _Logic and emotion are often at odds with one another,'_ Lilith had said when they last spoke.

Perhaps it was one of those things that would heal with time and she would eventually understand it. She certainly hoped so because she did not like this conflicted feeling or the sense of loss.

As for the small changes in her life, while not earth shattering at least some of it was annoying. It seemed that when the medications that had restricted her S2 organ from being fully active had been reduced, or when Dr. Ikari gave her back the bit of her/Lilith's soul that she had borrowed, with a little extra added boost...maybe because of all of the above...her body had underwent a short growth spurt. Not a lot, not enough to really be visible to the eye, but just enough to cause an annoyance.

Her clothes no longer fit properly.

The underwear and school uniform that lay in the usual heap she left them in the bottom of her locker were no longer comfortable. The uniform shirt had become too snug around her chest and shoulders and made it pucker and strain at the buttons just a little bit. The skirt felt tighter around her hips and behind and her underwear felt...constricting. Again, it wasn't much of a difference, but it was just enough of a change to be bothersome and annoying. Thus, she was not looking forward to putting on the plug suit.

It already fit like a second skin but at least it was a precise fit and once you were used to it, it was not uncomfortable. She could only imagine how it was going to feel and she did not need that added to the list of things that were currently already occupying her thoughts. This and her conflicted feelings about the Commander's demise aside, she had the spectre of an uncooperative Unit 00 before her.

She had received advice from both Lilith and Dr. Ikari on how to approach the problem. It would require confronting the issue with a certain amount of force and anger, something that surprisingly wasn't going to be hard for her to muster. Unit 00 had defied her when she was desperate and needed it the most. Because of its mocking lack of cooperation she had been unable to help Shinji when he was in danger and being hurt. That was unforgivable and she was not going to accept a repeat of that behaviour. She did not know what the soul was that resided in her Eva, if there even was one, but she could not and would not let whatever it was have things its way.

Unfolding the plug suit, she gave it one last disparaging look before resigning herself to the inevitable and putting it on. The results of pressing the button to shrink the suit to her form proved to be just as uncomfortable as she had feared, if not more so. She was being tightly squeezed rather thoroughly all over and was being pinched and squashed in certain select locations around her body and in a way that if it wasn't already somewhat painful, it definitely would be by the time she was done the activation test.

She considered the idea of simply taking it off once she got to Unit 00's cage and doing the test naked, but the life sign and monitoring equipment built into the suit were a necessary element she would not be allowed to go without. Especially not when one considered her Eva unit's unpredictable nature. She sighed, audibly, something that she rarely did. She would do what she had to do despite the discomfort it caused her, just as she always did. If this was the least of the discomfort she suffered today then she may consider herself fortunate.

Deliberately and rather stiffly, she walked out of the locker room and headed for the testing chamber.

* * *

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	25. Chapter 25

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

 **Transposed**

 _ **Chapter 25**_

The entirety of Kiel's estate was vast, taking up hundreds of acres of both forest and working farmland. Isolated within it, well away from the farming operations and surrounded by thick forest was the estate's manor, a huge mansion built with the enormous wealth Kiel had amassed through various means over the years. It was a grand, old, and beautiful structure befitting of the money spent on it and it didn't deserve to be owned by the scheming old bastard who had paid for its creation. Sadly, the place was also looking a little rough around the edges at the moment.

The grounds leading up to the structure were torn up in several places from the passage of vehicles and the exploding of several grenades. A couple of outbuildings were smouldering ruins and several of the doors and windows on the manor house itself were smashed and broken. The worst of the damage was to the newer annex at the back of the original manor house, an addition that had likely been made when Kiel had to start relying on a wheelchair to get around. While there had been battle damage to many parts of the house, this section had seen the heaviest fighting.

Pretty much every window was gone. The exterior and several interior doors were destroyed and the walls holed and shattered from bullets and grenade explosions. Burn marks marred the carpets and hardwood floors and the blood of the dead and wounded stained those surfaces as well. The defenders had outnumbered their attackers by at least two to one and had put up a decent fight but it was clear they weren't the best guns Kiel had in his employ. Most were now dead but several had either surrendered or been captured as wounded and were being tended to outside.

One of the victorious attackers, Matt Riker, strode down the main second floor hallway that cut through the annex and eventually ended up at Kiel's expansive office. The Benelli M4 shotgun canted over his right shoulder was ready for business just in case but the fight had been declared done well over an hour ago. He had just returned from the helicopter pad and maintenance barn that sat a couple of hundred yards back of the house. Some of the household staff had taken refuge back there when the fighting started. He was on his way back to Kiel's office where his partner had taken up residence, joining the search through Kiel's office while one of their techs took a crack at the computer on the huge oak desk.

Tugging at the neck of the tactical vest he was currently sweating under, he recalled the whirlwind that the last twenty four hours had been for them. As soon as word had reached Colonel McKinnley that the location of Kiel's private estate had been found and that he might be there, they had hopped on a UN transport and hightailed it for Germany, helping to plan the raid along the way by satellite feed and arriving just in time to take part in the final briefing before launching the attack. Unfortunately they had missed Kiel himself. He had left the estate that morning.

One would think that it would be reasonably common knowledge that the huge estate belonged to Kiel, but that wasn't the case. His name wasn't actually associated with the place, at least not publicly, and you had to dig very deeply through several layers of holding companies to find that he did indeed own it. In Germany and most of Europe for that matter Lorenz Kiel was known as a retired businessman and philanthropist who donated huge sums of money to the arts, education, and the medical community. Digging for information on him was regarded with disdain and suspicion and often resulted in a heads up being forwarded to the man or his staff.

Intel gathered from the hunt for the members of the Instrumentality Committee had eventually pointed them in the right direction and a great deal of digging went into determining that he had been spending a lot of time here recently and not in his more public residence near the NERV base in Berlin. Apparently even though Kiel held absolute control over them some members of the Committee hadn't been above trying to quietly dig for information on him themselves and they had proven to be a somewhat useful source of information. Those that were left at least. Kiel, the member for Russia and the member for China were still at large. Four others were dead and the rest were in custody and were singing like canaries after various levels and varieties of persuasion were applied, and certain facts were made known to them.

As he arrived at the double doors that led into Kiel's office, which were now missing their locks and handles courtesy of his shotgun from their room entry over an hour ago, he could see his partner perched on the edge of the desk and talking into their secure satellite phone and making her report to the Colonel. Her weapon for the raid, an HK 416A5 carbine was leaning against the desk, well within her reach. Two other raiders were looking through bookshelves and files while another was busy at the computer. He plopped himself down in one of the big overstuffed leather chairs in front of the desk, setting his shotgun in the other one to his right.

"Yes sir," she said into the phone. "We'll head back as soon as they get here. It's Miller's team anyway and he's more than capable of working with them. We'll just make introductions before we go to get things started." There was a pause as she listened for a moment. "We appreciate that sir, thank you." She hung up and set the unit down on the desk.

"We expecting company?" he asked.

"The Colonel said the Chancellor is sending a team from GSG-9 to take over the site and the prisoners," she told him. "Ehrlich's team by the way. She would have given us help on this raid if all of the teams hadn't been tied up elsewhere. Ehrlich's group is just coming back off a security op and will be diverting here instead of going back to base. We'll be leaving as soon as they get here. The Colonel has lined up a UN executive jet to get us back faster. We can grab a bite and a nap on the way back. Beats a cold cargo plane."

"Amen to that," he agreed. "Ehrlich will be pissed that he missed all the fun. And that bastard still owes us a round of beers but it looks like he'll be getting off the hook again."

She smirked. "You're just pissed that you won't get to flirt with his second and stare at her tits all night while we all get hammered."

"I wasn't staring at Mina's tits," he said, defending himself. "She's like five foot four and I have to look down all the time just to make sure I don't step on her. I can't help it if the view happens to be spectacular."

She rolled her eyes. "Too bad they weren't here for this. We could have used the Monkey to make clearing this floor a little easier. Would have distracted the defenders and split them up a little."

The second floor of the annex had been better defended than the rest of the house. Kiel's office was the prime target of the place so they reacted accordingly even though the old fart hadn't even been here. Mina 'Monkey' Krauss was a hand to hand combat expert and an infiltration specialist, a prodigy really. There wasn't anything that she couldn't climb and was invaluable when it came to getting into places and causing havoc. Extreme parkour and climbing anything in sight was how she relaxed and had fun. Martin Ehrlich was glad to have her on his team and as his second in command.

"It wasn't that bad, just time consuming," he said. "They had quantity but we had quality. I expected better personnel to be guarding Kiel than what we saw here."

"You think he took the better one's with him when he left?" she asked.

"If he did have better personnel then they must have already been gone," he answered. "The house staff wasn't very cooperative but they did say that Kiel and three other men left early this morning on his private helicopter. They either wouldn't tell me or didn't know where they were going, but I did manage to drag names out of them. One was Dr. Gerhard Holzer."

"That's NERV Germany's version of Dr. Akagi isn't it?" she asked.

"One in the same," he confirmed. "The names of the other two were Richard Schmidt and Conrad Dyson."

"Dyson!" she exclaimed. "I thought he was dead. It was reported that he and his entire mercenary group bought it somewhere in Africa."

"Wouldn't be the first time a supposedly dead merc resurfaced somewhere," he said. "Him especially. He's been listed as dead before."

"Wait a sec," the man at the computer said. "Did you say one guy's name was Richard Schmidt?"

"That ring a bell for you Miles?" he asked.

"Yeah," the tech answered. "When we were fishing around for info about Kiel we found a list of organizations that he donates money to. One was an outfit that helps reintegrate military personnel into civilian life. They offer medical and psychological services, help with job searches and living accommodations. Schmidt is one of the directors, it's called the Bittrich Foundation."

Riker looked at his partner. "Son of a bitch," he swore. "Underneath its shiny outer shell the Bittrich Foundation is a mercenary search and job placement service. They recruit and screen mercs for whoever is willing to pay their fee to find them. No one has ever been able or willing to go after them for it because the government itself has been known to hire mercs for jobs out of country that they don't want to be linked to. It's a dirty little secret that no one wants to bring into the open because it would bring way too many skeletons out of the closet."

"The records we found show that Kiel made two very large donations in the last month," Miles added.

"He's hiring himself a private army," Lake concluded.

Riker shrugged. "Pretty much has to since his access and ability to use the JSDF was taken away from him after we nabbed Matsuzaka and the Colonel met with the Prime Minister and the Secretary General."

"I wonder if they're in Japan yet?" she mused. "There's supposed to be one more Angel to come, would he want to risk the possibility of his assault force getting killed before that?"

"Unless he has control of the Seventeenth like one of Ikari's scenarios suggested, we have no idea when or if it might show up, especially since there is nothing there now to call to it and lure it in." He sighed. "We have no idea if it will show up a month from now, five seconds from now, or if it will appear at all."

"Fuck!" she swore viciously. "We're gonna have to go to a full alert status indefinitely and we're nowhere near ready yet to try and mount any kind of a meaningful defence of the base. This is going to turn into a complete cluster fuck, I just know it."

"There you go with that negative attitude again," he smirked, looking to stop her before she got too tightly wound. "No wonder no one likes you."

"Fuck off!" She threw the closest thing she could grab at him, which happened to be the satellite phone. He caught it easily.

"Tokyo 3 is nearly abandoned so it isn't going to be too hard to spot a bunch of outsiders if they come sniffing around," he said calmly. "We have more help coming from the UN and the Colonel is working with a couple of his contacts at the JSSDF to pull in some trustworthy help. Let the locals carry the bulk of the outside work, we'll concentrate on things inside the base. And even if it does turn into a cluster fuck..." he shrugged. "There's not much we can do about it. We've been there and done that so it won't be anything new. Seems to be our specialty."

"I know," she groused. "But it would be nice for once if things at least came close to staying on the rails."

"No fun in that," he deadpanned. "But if it was an easy job we wouldn't be the ones taking it on. We're literally going to save the entire world even if hardly anyone knows it. The outcome isn't in doubt, we _will_ do it. The rest is just details."

"No wonder I like working with you," she smirked. "You're an optimist and usually right too. Besides, its not like we could do anything less when three fourteen year old kids have been killing monsters and saving the world for months. It's our turn I'd say."

The sound of multiple helicopters approaching caught their attention. She stood and picked up her rifle. "Time to go." She looked back at Miles. "Let us know if you find anything interesting."

"Will do Captain," he responded.

Riker stood, dropping the shotgun over his shoulder again. As they walked out of the room he handed her back the satellite phone. "Think we could smuggle Ehrlich and Krauss back with us," he joked. "We could use the help."

"You wouldn't get an objection from them," she smiled. "Or me but I don't think even the Colonel could get us out of that mess if we did. The German Chancellor would be screaming for our heads."

He shrugged. "Oh well, after we take care of business we can collar Ehrlich for those beers and brag about how we saved the world without him."

"And you can stare at Mina's tits," she teased.

He shrugged and grinned. "Hey if there's a better reward for saving the world than beer and tits I don't know what it is."

* * *

 _ **NERV Tokyo-3, Eva Test Chamber**_

Sitting in the entry plug was no more comfortable than the walk to it had been for Rei, possibly less so because she was also now experiencing a return of the overall achy feeling she had had during and after her little growth spurt. She was not a happy Eva pilot right now and was experiencing a level of annoyance she had not known before. Perhaps it was partly due to the lower levels of mood levelling drugs in her system as they slowly weaned her off of them that was making her feel as such. It did make her wonder what she was going to be like in the future as the dosage kept getting lower to the point where she would finally be free of the drug's influence. She had been warned of the possible side effects and she was dreading the possibilities. Wild mood swings did not sound enjoyable.

"I'm sorry Rei," Dr. Akagi apologized, her face suddenly appearing on the cockpit video monitor. "The thought that you would need a new plug suit completely slipped my mind. We can always delay this until we get a new one made for you."

"I will manage," she answered. She had put up with far more discomfort in her life, though she couldn't remember being this irritated by any of it. "I wish to take care of this issue with Unit 00 as soon as possible."

"If you're sure then we'll begin the start up sequence," the Doctor said.

"I am sure," she confirmed.

Another video window opened, showing her Shinji from inside Unit 01. He was on standby in case her Eva went berserk and needed to be subdued. She felt some of her annoyance and discomfort ease a little when she saw him.

"Good luck Rei," he said. "I hope everything goes okay."

She smiled slightly which got her a smile back from him. "Thank you," she said quietly.

In his smile and his eyes however she could still sense the raggedness in him that had been present since the attack of the Fifteenth Angel. For the most part he seemed to be alright. Certainly he had become a little bit different than what she had known him to be since his mother returned, but there was something about him that had changed beyond that. Perhaps it was just the manner in which he was coping with the damage done to him and the agony he had felt. He may return to his usual self or it may remain with him for a long time...she did not know but seeing him changed because of it made her all the more determined to address her Eva's unacceptable refusal to help her come to his aid when he had needed her.

She put the chatter of the control room out of her mind as they went through the start up sequence and concentrated solely on the impending contact with whatever or whoever made up the soul of her Evangelion. Instead of waiting for it to make its presence known she sought it out. Even when the Eva was not powered up she could always feel whatever was within it and she could feel it a little more clearly now with the recent changes she had undergone.

She felt the surge as the Eva powered up but instead of the usual pull on her mind of contact being made it was as if the mind of the beast's inner soul lunged at her. The sensation was like being lunged at by a large animal with its teeth snapping at your face. Reflexively she jerked away breaking the contact but not before she felt the disdainful, mocking sneer within that contact. She hadn't even realized that she had let out a startled gasp until she heard Shinji's frantic, worry filled voice calling to her.

"The Eva's reaction startled me," she said by way of an answer.

"Are you alright Rei?" Dr. Ikari asked calmly.

"I am unharmed," she said. "I wish to try again."

Yui smirked slightly, detecting a little steel in the quiet girl's tone. It seems the Eva was making her angry and in this case that wasn't necessarily a bad thing. "Make it understand who is in control Rei," she advised her, reminding her of their earlier conversation with Lilith. "Like two wolves fighting for the position of Alpha, you have to show it that you are a bigger threat to it than it is to you. Show it your fangs Rei. You can do it."

"Yes," was her quiet, yet steely response.

Once again she shut out everything else and concentrated on the link. Even before the power came up she could feel the beast's savage amusement at her trying again, but she didn't give it time to act. This time and with the intent and the image in her mind to match as their souls collided, she went for its throat, ripping and tearing at the beast as she forced and imposed her will upon it. Her presence grew and she loomed large over it, dwarfing it within its own domain. Within the plug she leaned up and over the control yokes as wings of orange light sprouted from her back and her red eyes glowed.

The beast tried to fight back, the Eva twitched and strained in the mounts that kept it anchored to the testing room wall but it could not escape. Panic began to bleed to fear as Rei bore down ever harder and loomed ever larger before it. Something had awakened within the girl as she met its savagery with her own. The beast found itself backed into a corner with nowhere to run, no way to escape and with bared fangs at its throat and sharp claws at its heart.

"You have defied me for the last time," Rei all but growled. "You have broken my body and hurt me before but that pain was nothing compared to what I felt when you denied me the chance to help Shinji. You prolonged his suffering and you mocked my attempts to aid him. Such a thing will never happen again."

The soul of the Eva cringed in renewed fear as the claws at its heart began to slowly sink into its metaphysical flesh and the fangs at its throat came closer and seemed to grow longer and sharper. Rei's presence, her aura, continued to grow around it and push ever harder against it, threatening to crush it in a wave of pure will. No matter how hard it tried to push back it was being overwhelmed.

"You still seek to resist me?" Rei snarled. The Eva howled in pain and terror as the clawed fingers sank into its soul and seized its 'heart', the very core and essence of its being. "There are only two choices," she hissed coldly. "Yield or die."

Waiting inside Unit 01, Shinji couldn't help but feel worried for Rei. The battle she was fighting wasn't one that anyone could help her with. If she couldn't subjugate the soul of her Eva on her own it would never obey her. Even more worrisome was the nature of the battle. It wasn't physical and it wasn't even a clash of soul bodies within the Eva's inner world. It was a battle fought through the clash of consciousnesses during synchronization. It was a battle of thought and will.

He had been part of the conversation Rei had with his mother and Lilith, both so that he would know what was going on and so that he wouldn't worry so much as he stood by in case Unit 00 needed to be subdued. It hadn't really worked, he certainly was worried and while he had a great deal of trouble picturing Rei acting like an Alpha wolf to subdue her rogue Eva he certainly hoped that she could do just that. If she couldn't he would have to stop it when it went berserk. That wasn't something he'd be able to do without damaging it and hurting Rei in the process and that was the last thing he wanted to do. From her recent injuries to those she had the first time he met her, the images of her hurt and in pain were too vivid and he didn't want to be the cause of more.

 _'Have faith in her Shinji,'_ Lilith told him.

He wanted to, more than anything, but the straining, jerking, and growling of Unit 00 as it fought against its restraints increased his worry with every minute that passed. When it raised its head and let out a long, room shaking bellow his heart leaped into his throat. When it went silent and slumped against its restraints he couldn't take the silence that followed it.

"Rei!" he called out. "Rei are you alright?!" He only knew the comm channel was open because he could hear the sound of her breathing heavily over the link. "Rei?"

"I am alright," she finally answered. "There will be no further problems with Unit 00's behaviour."

"Well done Rei," Yui congratulated her.

"Yes, good job Rei," Ritsuko chimed in. "And thank you for all of the fascinating data you generated for us. You've given us some interesting things to study. Catch your breath then we'll get you out of there. After a quick debrief you can go get cleaned up. We'll do a sync test after we get a new plug suit made for you."

"We're all done now Shinji so you can get out and go shower up," Yui said.

"Okay," he answered, his eyes still on Unit 00.

 _'Relax Shinji,'_ Lilith told him. _'Rei really is fine, she's just tired.'_

 _'I'm sorry,'_ he apologized. _'I was afraid I would have to fight it with Rei trapped inside.'_ He didn't need anything close to a repeat of the incident with the 13th Angel. He had enough things he felt guilt over and more than enough things to give him nightmares now as it was.

 _'There is nothing to be sorry about Shinji,'_ she softly assured him as Unit 01 began to shut down. _'It is understandable that you would feel that way but it is done now and Rei has regained mastery of her Eva. Go and have a nice long hot shower and let yourself unwind."_

 _'Just wash your troubles down the drain Shinji!'_ Misato cheerfully called out to him.

He couldn't help but chuckle a little at her infectious tone. ' _Okay Misato. I'll talk to both of you next time.'_

 _'You can talk to us now whenever you like Shinji,'_ Lilith reminded him. _'You have the same connection with me now that I have with your Mother. I can even be a bridge for you to speak to Rei this way as well.'_

He had forgotten about that, or more accurately he hadn't really taken the time to think about it after Lilith had spoken to him during the incident with his Mother down in Terminal Dogma. He smiled. Lilith was proving to be another important person in his life just like his mother, Misato, and Rei were and he was glad that he could talk to her at other times now without having to be inside the entry plug.

 _'Thank you,'_ he thought happily as the LCL began to drain from the plug.

 _'Don't do anything naughty in the shower now,'_ Misato teased in a sing song voice.

 _'Misato!'_

It was almost a half hour later when Rei was making her way to the locker rooms, thankful that the debrief had indeed been short. Her patience at being shrink wrapped in her ill fitting plug suit had pretty much reached its end and she also felt rather drained both physically and mentally from her confrontation with Unit 00. Using her AT field as she had and pushing her mental presence upon the Eva's inner spirit as much as she needed to was very taxing. Even so, she felt a great sense of relief that the ordeal was over. She had asserted her dominance over the beast and there should be no further issue. Thus, a nice hot shower and then getting into some much looser clothes and getting some sleep sounded very pleasing to her right now.

Upon entering the locker room she pressed the button on her wrist to expand her plug suit, coming to a sudden halt when nothing happened. Frowning slightly she tried again with still no results. The frown turned to a scowl and she stabbed harshly at the button several times to no avail. She closed her eyes and took a calming breath to quell her frustration. If she could not get the suit to loosen, then she would just have to unzip it, there was little point in getting upset about it. Either her fatigue or the lessened effects of the mood altering drugs were affecting her rational thought. It was rather disconcerting.

She pulled on the zipper's small tab and it didn't move. She raised her chin and with her free hand she pulled up on the suit's collar to make sure it was straight and pulled again. It still would not budge. She tried several more times, up and down, side to side, twisting and pulling but it still would not move. She hung her head in frustration and defeat. Apparently she was not going to be able to escape the accursed garment without help. It was then that she noticed the sound of the shower running on the other side of the curtain that separated the male and female designated sides of the locker room.

Shinji-kun was still here. He would help her.

Without hesitation she pushed aside the curtain and crossed the threshold, following the sound of the water and heading for the plume of steam rising out of the third stall in line from the end. Upon reaching the end of the open shower stall she found Shinji standing under the heated spray, eyes closed and a slight relaxed smile on his face as the water pelted the back of his head, neck, and shoulders. Something that she herself was looking forward to doing...if she could escape her malfunctioning plug suit. She didn't really want to disturb the peace he seemed to be enjoying but she needed his help.

"Shinji," she called.

His eyes shot open. "Yeaaahh!" He stumbled back under the water, luckily regaining his balance and not falling. He stepped back forward again, wiping water from his face. "R-Rei...what are you doing here?" A moment later his face turned red as he realized the situation and covered his young manhood with both hands.

 _'Little late for that doncha think Shin-chan?'_ Misato's voice sang in his head, clearly amused. _'She's seen you naked already before this.'_ It didn't help that he could also hear Lilith snickering in the background.

"I require your assistance," she said simply. She noticed that he moved his hands away and for some reason she found that to be quite acceptable though she was entirely sure why. She chalked it up as just another of the odd mix of things she had been thinking and feeling lately. She poked at the controls on her wrist. "My plug suit is malfunctioning and will not loosen. The zipper also seems to be stuck and will not move."

"I...um...okay," he stammered. "L-let me have a look." He stepped up closer to her, though not _too_ close. Rei raised her chin and he grasped the tab on the zipper and moved it around. "It looks like some of the teeth are bent and a couple of them have come out of the clasp."

"Can you undo it?" she asked, the tone of her voice sounding as much like pleading, something he had never heard in her usually even and inflection-less manner of speaking. "It is very uncomfortable."

"I-I'll try." Grasping the clasp with his right hand, he used the thumb and forefinger of his left to pinch as much of the material as he could get a hold of and tried to work the exposed teeth back into the clasp and hopefully get the zipper to work. Unfortunately the device was not going to cooperate. The teeth of the zipper began to separate and given the tension on it from how tight the suit was, it kept on separating until it reached the bottom, coming completely undone except for the half an inch or so at the top where the clasp still held it together. As the garment spread open Shinji got an eyeful of smooth, pale white flesh from Rei's now partially exposed breasts all the way down to the little tuft of blue hair peeking out just above the bottom of the zipper. Needless to say his face went bright red despite having seen more than this of her before. There was just something about the sight of her partially clothed in the skin tight suit that got to him.

Despite still being stuck in the suit Rei felt a measure of relief. It was easier to breathe now but from the waist down she was still very uncomfortable. She looked to Shinji who had taken a step back. It was obvious that he was nervous and his face was very red, yet his eyes still seemed to be fixed upon her bared flesh and it seemed that a certain part of his anatomy was responding to the stimuli. She thought it odd that he had not turned so red or had stared so fixedly at her when she was fully naked. She found that she did not mind him looking at her like this nor did she mind the obvious physical reaction he was having.

Apparently it was yet another effect of the lessened amount of mood altering compounds in her system. There was a tingling sensation going through her body as she gazed upon him and thought of how the current site of her was affecting him. Was this how physical attraction felt? She knew that she was already attracted to him emotionally with what little free emotion she was able to feel now. With previous and ongoing mood and emotional swings, as mild as they had been thus far and with her current fatigue, she was feeling a little frazzled.

"Shinji-kun," she called as she grasped the still stuck clasp.

His head shot up and his eyes went wide. "I-I 'm sorry Rei!" he blurted out. "I d-didn't mean for that to happen and I didn't mean to stare at you. I'm sorry!"

"It is fine,"she assured him. "I do not mind," she added much more quietly. "However, I am still stuck in this suit. You will have to pull the clasp apart or else I still will not be able to take it off."

Hesitantly he went to step forward but stopped when he suddenly realized that he had gotten hard while staring at her. With a look of shame on his face he covered himself once again and lowered his head. "I'm sorry," he croaked pitifully, sure that she would think him a disgusting beast now.

She stepped toward him. "Shinji." Her voice was firm but she did manage to keep the frustration and the tiny bit of stiff annoyance out of her tone. Even so he still flinched. He was not the object of her displeasure but she was at her limit with how things had been going today. Still, it did not make her feel good that she had made him react like that.

"You have done nothing wrong," she assured him. "And I am not upset that you were looking at me nor am I upset that you had the reaction that you did."

"Are...are you sure?" he asked uncertainly, slowly raising his head to look at her.

"Yes," she answered simply.

Swallowing the large lump in his throat he raised his shaking hands to the collar of her suit. The light touch of his fingers left warm traces on her skin as he curled his fingers into the fabric. She could tell that he seemed worried about the contact but at least he didn't stutter out another apology. Taking a firm grasp on the material he began to pull to either side. She raised her chin again to avoid a possible hit when the stubborn clasp finally let go. It took a couple of moments and some wiggling around but finally the remaining teeth came free of the clasp. The force of his pulling caused him to pull the top of the suit wide open rather abruptly, even pulling it off her shoulders and partway down her arms.

 _'Oh my, so forceful Shinji-kun,'_ Misato gushed. _'Just tearing her suit open like that to expose her lush and firm young breasts!'_

"Misato!" he exclaimed out loud.

Rei had heard her words as well and could feel her cheeks warming. Truthfully, she had felt a slight trill of something...excitement?...flash though her when he pulled the suit open so abruptly. "Major Katsuragi is very strange," she deadpanned.

"You can say that again," Shinji muttered. Misato's response was a giggle.

Rei began to try and pull her arms out of the sleeves but the suit was still too tight. She grasped the glove on the left with her right hand and tried to pull her hand out of it but made little progress. She sighed.

"It seems that I still require your assistance Shinji." She turned so her back was to him. "You will have to pull downwards."

He swallowed again, seeing the problem. He was literally going to have to peel the suit off of her, more or less turning it inside out as it came off. Grasping the top of the suit he began to pull downward, slowly revealing her arms and her back, all the while trying to ignore the fact that he was quite literally undressing her.

When the suit got down to her hips he had to go to his knees to be able to pull it any further and blushed furiously as he found himself up close and pretty much at eye level with that cute rear end he had shamefully admired numerous time while it was squeezed into the plug suit. The suit stopped moving at the top of her thighs and he immediately saw why. The sleeves had pulled tight, stopping his progress. Her hands were still caught in the gloves, the reason being the collar around the wrists that held the controls for the suit. There was no way to pull her hand back through it without the suit being expanded.

She did something he had never seen her do before. Her shoulders slumped and she sighed in something akin to defeat...before lashing out and smashing the collar around her left wrist against the end of the rigid shower stall. Twice. The arm fell back loosely at her side and he could practically feel the aura of defeat and resignation coming off of her, it was something he knew all too well after all. He wanted to say something but exactly what that was escaped him, making him feel just as useless as he ever had. After a moment of silence but for the continuing sound of the water from the shower, there was a sputtering, strangled hissing sound and slowly the suit finally loosened up.

She wasted no time bending over and shoving the suit the rest of the way down her legs, leaving him with a face full of the most intimate part of her. Either Lilith or Misato said something at that point, but he completely missed it. Coming to his senses he stood and stepped back, his face burning as if it had caught fire. He watched as Rei, finally now free of the suit just stood staring at it for a moment, before shocking him again and kicking it several feet away. She turned and stalked toward him. Automatically, sadly, he stepped back, finding himself passing under the running shower head but that was where Rei stopped. He heard a barely audible sound of contentment pass her lips as the hot water came down on her head, neck, and shoulders. He became ashamed of himself when his eyes seemed to fixate on the sight of rivulets of water running down her chest and over the peaks of her breasts.

"I-I'll let you have the shower to yourself Rei," he stuttered in his self recrimination. She did not need to be stuck in here with him when he was unable to keep from ogling her or having his body react like he was some pervert. Before he could even try to get past her and exit the stall though, her hands landed on his shoulders and gently held him in place. He reluctantly met her gaze, sure that she must be upset with him but he was surprised to see that she was actually smiling slightly and her pretty red eyes were looking directly into his.

"Thank you for helping me Shinji," she said softly.

"Oh...um...sure..."

She surprised him again for the third time in the last few minutes when she slid her arms under his and wrapped them around him, gently pulling him flush against her. His whole body went rigid as he felt her soft breasts pressed against his chest and his hard member pressed against her lower abdomen.

"I have heard that a hug can make one feel better," she said quietly in his ear. "I wished to find out if this was true."

He could attest to the power of a hug. Nothing could chase away his angst and uncertainty more than a hug from his Mom or even Misato. It occurred to him that Rei had never had anyone in her life who would ever even try to comfort her in such a way and he knew enough now about how she had been feeling in recent weeks that she could probably use some comforting. He wasn't sure if he was the right choice for that but he found himself feeling like this was another of those things he could not run away from. So, he gently wrapped his arms around her and held her in return.

"Yeah, hugs are good," he said.

After a moment they both relaxed.

"Yes, they are," she agreed.

He didn't have to see the smile on her face to know it was there.

* * *

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	26. Chapter 26

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

 **Transposed**

 _ **Chapter 26**_

 _ **Five Days Later, Somewhere in the South China Sea**_

To the eyes of most, the large freighter looked pretty much like any other cargo ship plying the sea lanes of the area. Like many it was an older vessel but it had been well maintained. It needed a little fresh paint here and there with weathered and rusty patches dotting its hull and superstructure. A discerning eye would find the number of various aerials and dishes on the ship's superstructure to be suspicious, indicating that perhaps it was not just a simple cargo vessel and the same could be said of the reconfigurable helicopter pad at the stern. The real proof that it was something more than it looked would be the five inch naval gun concealed beneath said helicopter pad, and the second one at the bow hidden within an old, weather beaten shipping container.

In truth the ship had three functions. One was to deliver sensitive cargo for SEELE and Lorenz Kiel in particular. The second was to act as a listening post and electronic surveillance vessel, and a very powerful one at that. Quite a bit of useful information had been gathered by it. The third function was to act as a mobile base and safe house for Kiel himself, a function it was currently filling.

Below decks in what was once a part of the larger cargo hold, there was a conference room that doubled as Kiel's office. While not as luxurious as his offices at home it was well outfitted with a sturdy table with a desk built into one end. There was dark wood panelling on the walls and to one side there was a wet bar and a table set up with both a coffee and tea service. Kiel was at the desk at the end of the table while two of the dozen high backed leather rolling chairs, one on either side of the table, was filled by the remaining members of the Instrumentality Committee.

To his left was a thin, bald man. He was the Chinese representative, Yu Zhe, a former General in the People's Army who used his influence and connections to manipulate key figures in the government and build his own personal empire. He was well entrenched by the time of his retirement from the military several years before Second Impact. To his right was the tall, stocky, and greying Russian representative, Dmitry Petrov. A highly successful businessman and practically the godfather of the Russian _mafiya,_ his illegal activities probably netted him as much or more than his legitimate ones. He dealt in salvage and plunder, bringing out usable currency, precious metals, and gems from banks, depositories, and diamond exchanges in coastal cities that had been lost and flooded during Second Impact. A real parasite of misery.

"Be calm?" Petrov growled. "We are all that is left, the wolves are snapping at our heels, the project is in ruins, and you tell me to be calm?"

Zhe turned to the Russian. "If the Chairman has told you to be calm Dmitry, it is because the project must still be viable. Am I correct Chairman?"

"You are," Kiel answered. "There have always been variables to the core plan that could be pursued to accomplish the same end. Their percentage chances of success are lower but they are still viable alternatives."

"Then why are we just hearing of this now?" Petrov asked.

"For one of the very reasons we find ourselves in the situation we are currently in," Kiel answered. "It is a fact that at least one of our captured members and probably more has been telling the SIS everything they know. You know the personalities of the others as well as I do. You know that the potential was always there should certain members find themselves in such a position. The risk of this information being known before it was needed was not an acceptable one."

"We have already lost one and possibly two of the mass production units," Zhe said. "One has been confirmed as captured and the facility shut down, the second is probable since we have lost contact with the facility. How many can we lose and still reach our goal?"

"The more units we have, the higher the chance of success," Kiel began. "But we could lose eight of the nine so long as the unit I control is still at large. It has been modified to handle the task alone if it must."

"That's very convenient Chairman," Petrov said, his voice laced with suspicion. "Having the one unit that can perform the task on its own being under your control."

"Would you prefer the alternative of having no options left?" Kiel asked coldly.

"I would prefer the plan to be operating as it should be, as we have been assured that it would," he shot back.

"As would I but it is obvious that this is not possible now," Zhe countered. "We had been fortunate that the scenario had gone as well as it had with little need for adjustments even with whatever machinations Ikari was up to."

"It was Ikari who broke open this hornet's nest!" Petrov exclaimed, slamming his fist on the table. "Who else could have given that useless triple agent the information to take to the SIS? He should have been replaced when we first became suspicious of him!"

"And who would we have replaced him with?" Zhe asked tightly. Petrov's paranoia and lack of reason was irritating him as it always did.

"Ikari was an acceptable and manageable risk," Kiel said, letting some iron into his voice. He was reaching the end of his patience. "No matter what game he was playing there was no advantage for him until the Angels were defeated and there were measures in place to deal with him and keep the scenario on track."

"That train left the track long ago!" Petrov snarled. "When Yui Ikari returned from the Evangelion's core we should have stepped in then!"

"You are speaking from the view of hindsight Dmitry," Zhe scolded. "Dr. Ikari's return was something that could not be accounted for since it should have been impossible and Gendo's reaction could hardly be predicted. Even so SEELE had more than enough influence and people in place to suppress the issue or limit the damage at least."

"If Matsuzaka had been paying attention to business instead of fucking his mistress then that spy never would have made it out of Tokyo 3 let alone get to Tokyo 2 and hand off what he had!" Petrov ranted.

"Just as the actions of most of the Committee have led to our downfall and need to hide out like rats," Kiel snarled at the Russian. "By panicking like scared children they have exposed us when they should have held firm and trusted in everything we have built and planned for. You are no better Petrov, your plundering of the sunken cities has garnered too much attention from the SIS and other agencies all over the world. How many times has the organization had to cover your tracks just to keep the wolves outside the door?"

Petrov was caught in a state between outrage and fear. He could not refute what Kiel said. His illicit activities had brought too much attention, though he blamed it on underlings being careless and had taken care of them accordingly. It wasn't like he was the only one the organization had needed to shield. That smug bastard Zhe trafficked in human flesh and had a thing for teenage girls. _Young_ teenage girls, which disgusted him to no end. But at least SEELE had only had to clean up behind him once. Word through the grapevine had it that not only had Zhe purged the people responsible for the issue in a very gruesome and drawn out fashion, he had also purged their families and made sure that everyone knew that any further screw ups would result in the same happening to them.

"Perhaps we should take a break," Zhe suggested, as always trying to sound like the voice of calm reason. While he hated the Russian with a passion, he feared the consequences of crossing Kiel even more, especially now since they were reliant upon him for their continued survival until the plan came to its fruition. "Some fresh sea air would do us good, help clear our minds and get us back on track. You can smoke one of your hideous cigars Dmitry without offending anyone." He looked to Kiel.

"A sound idea," the old cyborg acquiesced with a nod. "By all means."

Zhe politely inclined his head and rose from his seat. Petrov simply grunted but joined the Chinese representative in leaving the conference room and heading topside.

Kiel picked up the phone on his desk and punched in a two digit number, calling his chief bodyguard Josef.

"Yes sir?" came the gravelly voiced answer when the line was picked up after one ring.

"They are headed topside," Kiel informed him. "Take care of them please."

"As you wish sir."

Kiel hung up, leaned back in his chair and sipped from the coffee mug that had been sitting in front of him. Something stronger might be in order but it was still a bit early for that. Within a few minutes Zhe and Petrov would have their bellies slit open and be dumped overboard to further feed the sharks that were already dining on the bodyguards they had brought with them. Their helicopter would then be shoved overboard and allowed to sink into the sea, making room on the pad for his own which would be returning later.

He was glad to finally be rid of them, of all of the Committee members. They had been a tolerated but necessary evil. In order for his plans to work he needed an organization that could exercise influence over a great many of the world's countries and their leaders as well as the UN. While each member of the Committee was ridiculously rich, even collectively they did not have the necessary financial wherewithal to fund everything that was needed to make his plan succeed. The Evangelions, the MAGI computers, bases all over the world and the might of Tokyo 3 in particular cost trillions, never mind the cost of repairing battle damage.

Keeping all of the members of the Instrumentality Committee corralled and in line was a headache, but it was a headache he had counted on and knew he had to endure. Managing a collection personalities was always difficult and that task was made even more onerous since they were all very rich and powerful men with the enormous egos to match. Add in the fact that some had been or still were rivals in business and the distrust and hatreds of a few over nationalities and it looked like an impossible task. However, he had the skills and the strength of personality to make them see and understand in no uncertain terms just exactly who was in charge and that he would not tolerate disruptions to the scenario.

The biggest wild card had always been Gendo Ikari but he was also one of the most important parts of the puzzle, being tasked with making sure the spawn of Adam met their demise. He had always suspected Ikari of having machinations of his own but never knew precisely what the man was up to despite the number of eyes inside the the Tokyo 3 base. The most logical assumptions were that he was either working towards preventing Instrumentality, or trying to take it over for his own reasons. What those reasons may be were something he hadn't been able to figure out, at least not until Yui Ikari returned from the core of Unit-01 and Kaji Ryouji made his trek to Tokyo 2 and put the information in the hands of the UNIO SIS team.

He agreed with Petrov that Gendo was the only one who could have given that information to Kaji. Fuyutsuki was a follower, playing out the string that was the rest of his life. The strength of his convictions had not been enough to override his fear of death and he had joined Ikari as his right hand rather than go public with the truth of Second Impact. Akagi was just as unlikely. She was a desperate woman clinging to any sign of affection and attention, or the illusion thereof that Gendo would show her and was too afraid of losing it before the end to ever go against him or SEELE.

The timing of it made him believe that if Gendo was indeed trying to subvert Instrumentality to his own desires, it had something to do with his wife. Perhaps he thought he could somehow be reunited with her if he had control of Instrumentality. The man had done a masterful job of not showing any public indication of the grief he had over losing his wife to the contact experiment but he knew to at least some degree that it was there. Even Gendo could not escape every eye that was upon him and he had seen enough in the man's behaviour shortly after the event to know better. In hindsight, some of the man's actions and ploys made more sense now.

It hadn't mattered however and still wouldn't at this stage even if Gendo was dead. He did not have absolute proof and information had been very hard to come by ever since the damned SIS had arrived at NERV HQ, but all indications he had received told him that Ikari was dead. He didn't know how he had planned to take control of Instrumentality but it didn't matter now at this stage. It didn't matter that now the remainder of the command staff at NERV HQ would be trying to stop it. It didn't even matter that he seemed to have lost the ability to have the Japanese government turn on them and send in troops. He had more than enough highly paid and thus highly motivated mercenaries to throw against them to do what he required.

Should the mercenaries fail and not at least neutralize the pilots, there was little hope of them fighting off the mass production models even if he did not have all of them at his disposal when it came time to launch them. Even Unit 01 should be no match for multiple MPE's. The Third Child had racked up an impressive record but his combat skills were not up to par to be able to match the mass produced units. Even if it went berserk it should still be brought to heel soon enough. Unit 00 he saw as even less of a threat. While the First Child was better trained and more capable that the Third, her ability to sync with her Eva was considerably lower. Unit 02...it might as well be a paperweight with its pilot having lost her marbles and still residing on a hospital room. It was no threat.

He set down his coffee cup and rubbed the new lump on the left side of his chest through his heavy suit coat. The last remnant of Adam, it would be his conduit for regaining all that had been taken from him when he had been subjected to this punishment. Finally the end to his personal hell was in sight. Soon he would be able to cast off this decrepit shell and return to what he once was, free to resume his life and his quest to create a being that shared the properties of both the Fruit of Life and the Fruit of Knowledge. The rest of his kind would not be pleased with what he had done here or with his escape but he did not care. They would never find him unless he wished to be found and he would have all the time he desired to perfect his vision of creating the perfect being to seed worlds with. A being that would survive any threat to it through both intelligence and might, and he would guide those beings in the ways his brethren stubbornly refused to.

"Almost there," he said aloud. "After so long I am almost free."

For the first time in ages a genuine smile came to his withered old lips.

* * *

 _ **Dr. Akagi's Office**_

Maya Ibuki raised her arms above her head and stretched, trying to alleviate the ache she was getting between her shoulder blades from spending too much time hunched over the keyboard of her computer. All the while though she was keeping an eye on the activity on her screen.

"This one is taking their time instead of trying to bull their way in," she said.

"Maybe someone is finally getting serious," Ritsuko said from the other side the desk where she had a pair of screens set up. She turned and took a quick look to the one on her right which was showing the same thing as Maya's. "The last several attempts to hack in looked like someone let their kids loose on the system. Probably a ruse to make us lazy since they would know we wouldn't take it as serious or even a remotely worrisome attempt."

"This one looks more focused and patient," Maya observed.

Over the last couple of days they had seen an increase of hacking attempts of various strengths. Ever since the MAGI had first went online there had always been attempts to hack it for any number of reasons ranging from serious attempts to infiltrate and steal info or do damage, to hackers trying to break in just for the hell of it and to see if they could. Many of the recent attempts looked like little more than amateur attempts and hadn't even been much of a nuisance.

At first glance it seemed like nothing but the periodic rise in activity they were used to seeing on occasion. But since they were expecting something like this they carefully charted and monitored every attempt and what areas of the system were being targeted and it didn't take long for a pattern to show itself. So, they began revealing the bait they had already placed in the system, but they didn't make it simple or obvious. The hackers had to work for any ground they seemed to gain and were fooled into believing they had achieved something on their own rather than having been allowed in.

While they were snooping and Maya led them around and played with them, Ritsuko back hacked them and found their locations, leaving a nasty little surprise behind for them if they tried hacking them from that machine again. Thus far it looked like the machines used were spread all over the world and some may have been hacked themselves to perform the intrusion into their systems. Sooner or later they would get to the root of it. They had been giving their adversary enough of a taste of success that at some point they would make a serious attempt.

Maya suddenly sat up straight in her chair and started clacking away at her keyboard. "Here we go, they're starting to get serious now. They've picked up the pace and are starting to move into the pathways we set up for them."

"Well that proves that they are the same ones who were probing us in those other attempts," Ritsuko smirked. "Give them your best Maya and lead them on a merry chase. Make them earn it hard." She cracked her knuckles. "I'm going to start back down their trail and find out who this is."

"You got it Sempai!" the younger girl chirped enthusiastically. She loved this, it was exciting and she was doing what she loved best, working in concert with her mentor. The amount of work they had done since starting on this project was staggering considering the time frame it had been accomplished in. They had both been able to get creative and add in a little malicious intent. It was just like when she used to counter hack people in college only with far greater stakes and she couldn't deny the guilty pleasure of the thrill it was giving her to lead their enemies around by the nose and make them dance to her tune. It was a level of power and confidence she could never show outside of the electronic world.

Ritsuko smirked as she raced along the hacker's back trail. The gleam in her proteges eyes as she ran the hacker ragged was amusing. She had been totally surprised when Maya had sheepishly admitted to her that she was a hacker, less surprised that she tended to go after the ones that tried to cause damage and chaos.

Maya the cyber hero...who would have thought. She was impressed though because she was very good at it and for someone who was as meek and gentle as she was, she certainly could come up with some nasty surprises for someone on the other end of her hack. Which was exactly the kind of thinking they needed right now. They would have to be aggressive and hit back hard and fast if they were to keep the MAGI from being overtaken.

The MAGI may have been her mother's creation, but she had done more than her fair share to upgrade it and enhance it and it was a point of pride for her to keep SEELE's hackers out of it. The pilots had borne the brunt of this war thus far, a war they were supposed to lose in the end and she had been stupid enough to help bring them toward that end. Now it was her turn to try and work towards her redemption, if there was such a thing for her, and take on this battle. If the plans she and Maya had devised worked they would be luring the enemy onto terrain of their choosing and then attacking them from favourable ground. As a matter of fact it had already started.

They had planted viral seeds in a number of subsystems that were connected to the other MAGI computers across the world and using back doors that she was able to discover after looking through her mother's notes she had left a few surprises on the periphery of the MAGI systems themselves. But this current back hack she was attempting could yield much more if it turned out to be coming from or through one of the other MAGI and not somewhere else. She hoped to sneak into the enemy camp while they were snooping into her systems and leave behind some very nasty and malicious code that they could activate when the real attack came against Tokyo 3.

"Sempai..." Maya began, sounding a little strained as she typed away furiously. "I think we might have two hackers in here. It's all I can do to stay ahead of this."

Ritsuko turned to the machine on her right and saw what was going on and jumped into the action. "One's leading and the other is following, looking for other routes in their wake. Not entirely unexpected. I'm going to steer them into the maze. If they take the bait that's in there they'll be doing us a favour."

With a series of keystrokes she routed the second intruder into something they had decided to call the maze. It was a cache of old data files that went all the way back to NERV's days when it was known as GEHIRN. There was a link to an old server in there that had relatively weak protection on it and could easily be mistaken as something that had been missed and forgotten long ago as systems were changed over and upgraded.

"Once you get the alert that the second hacker hit that old server, start hitting your playmate with some more robust defensive measures," Ritsuko instructed. "By then they should have taken enough bait and be more than ready to scurry back to their hole."

"Got it Sempai," Maya responded.

Ritsuko went back to her own hack. She was getting closer, she was in the country of origin now and that gave her a pretty good idea of who at least one of their hackers was so she took a gamble and diverted her search on a hunch. It paid dividends almost immediately, right about at the same moment she heard a chime sound on Maya's terminal signalling that the old server had just been hit. She recognized the security measures she was running into. Jackpot.

"Starting to hit this one now Sempai, they should be backing out any second," she reported.

"I got the bastards!" Ritsuko exclaimed in uncharacteristic excitement. "They're in America...Massachusetts. First one is at MIT and the second one is coming from the MAGI at NERV's First Branch!"

She attacked her keyboard like she was possessed, fingers flying just as fast as they had been when she raced against time to stop the 11th Angel from taking over the MAGI and initiating the self destruct. With her hunch proven she raced through the back doors into the system and planted her packets of malicious code. When they activated they would spread to any of the other enemy MAGI systems connected with the First Branch for the attack. If it worked as they designed it to it would initiate a flood of useless data to clog things up and unleash a truly insidious virus that would require all of their attention to attempt to stop it. It should stop their attack on the Tokyo 3 MAGI and with the improved firewalls and early warning measures they had put in place, they should be able to activate it before any serious damage could be done.

"They're out of our system," Maya announced.

"I'm out of their systems and..." Ritsuko began. The pause seemed to go on for an excruciatingly long time. "I'm clear. No signs that I was detected."

They both slumped in their chairs in relief, feeling the adrenaline drain hit them. Though they didn't breathe completely easy just yet as they kept a close eye on the monitors for a few more minutes just to make sure they were truly in the clear.

"We did it Maya," Ritsuko finally said with a tired smile. Neither of them had gotten much sleep over the last couple of days. "We got them good. There are a few other things we can still do but this should keep them from being able to take over our MAGI."

Maya let out a long, sighing breath. "That's a relief. I feel like I've been holding my breath for the last few days dealing with all the hacking attempts and knowing that this was coming."

"You've done an outstanding job Maya," Ritsuko said. "You're help has been invaluable, none of this would be in place without all of your hard work and input."

"T-thank you Sempai."

Ritsuko did her best not to chuckle and further embarrass the girl as her face reddened at the praise. Red cheeked and bashful Maya was just too cute and she allowed herself a wistful smile. Even with all that she had learned lately and with the pressure they were under, Maya still maintained that air of innocence and youthful idealism about her. What she wouldn't give to be something close to that again herself but she had already sold her soul to a devil and there was no bargain to be made for its tattered remains even now that said devil was dead.

She couldn't deny however that working so much and so closely with Maya lately had been good for her. So had working to save the world rather than trying to destroy it. That in itself was a significant notion for her since when she had been blindly following Gendo's plans she hadn't actually cared one way or the other about the fate of the world. Like Gendo she had seen the world as being a miserable place but she hadn't been actively seeking out its destruction. Her apathy about the continuance of human life was the feeling that the world held nothing for her beyond her flawed infatuation with a man that didn't love her.

However that feeling seemed to have left her and there were two specific reasons, or more precisely two specific people that she could attribute it to. Yui Ikari and Maya Ibuki. She had never known Yui but had spent years despising her. Even though she was gone she was still the most important thing to Gendo and she meant nothing to him. When Yui emerged from the Eva's core she grew afraid of the woman. Afraid of what she would think of the obviously sick woman who had been so desperately chasing her husband's coat tails.

Imagine her surprise when Yui turned out to be one of the most genuinely nice people she had ever met. Now she saw where Shinji got it from. It seemed he had gotten all of his best traits from his mother. Yui didn't look down on her but saw her as a victim of Gendo's machinations and gave her both a chance and a reason to turn against the plans she had been so much a part of. She had also easily befriended her and she had most certainly needed a friend. She had been doing a fine job of screwing up her friendship with Misato and then the crazy purple head goes and gets herself sucked into the Eva. But the woman she had never known but despised and feared anyway had saved her from falling into a bottomless pit of loneliness, despair, and from just giving up completely.

She wondered if involving Maya was part of her plan or if fate had just conspired to make sure she was outside the door at just the right time to hear some ugly truth. Maya had quickly become the very thing that kept her from sliding down the slope and into the abyss when her thoughts became too dark. The girl had forgiven her, kept her upright when she felt like she was going to fall and was a warm, bright light in the darkness she had lived in for so long. Never mind work, Maya had become very important to her on a personal level.

And that was scaring the hell out of her.

She didn't know if the growing feelings she was having for the younger woman were genuine or the continuing byproduct of her desperation to be loved which had gotten her into this entire mess to begin with. She didn't want it to be that because Maya deserved better. She was pretty sure there was some truth to the gossip and teasing that made the rounds about Maya's devotion to her Sempai and if there was ever anything between them that way she wanted it to be genuine, for Maya's genuine feelings to be returned in kind. Why she was feeling what she did was only part of the equation though, the other part was the fact that she may be having feelings for another woman. It wasn't something she had ever really given much thought to before.

Sure, she and Misato had fooled around a little once in college, drunk off their asses at the time no doubt, but even then she hadn't thought much about it after that. Would it really be so bad if Maya felt that way about her, or if she found that she really did feel the same way about Maya? Above all else wasn't being truly loved by someone what she had been seeking so desperately?

She really was pathetic, it was too soon to be worrying about this. She needed time to figure it out and there would be plenty of time for that _if_ they survived what was to come. If they did survive maybe she would feel that she had earned some small measure of redemption and would be worthy of Maya's feelings and be able to figure out her own.

She stood and stretched, her back and shoulders making several pops and snaps. She walked over to the couch that had been her bed on far too many occasions and flopped down at one end.

"I think we're long overdue for a lengthy break," she said with a sigh. "I could use a shower, some decent food, and a few hours of sleep."

"Well we are ahead of where we thought we would be at this point," Maya said as she got up and went to the small fridge across the room and retrieved two bottles of water for them. "Now that they've decided to evacuate the city I guess we can't really go home though." She handed Ritsuko a bottle and sat down next to her.

"They said at the meeting this morning that they are going to allow the personnel that will be staying to go to their homes and pick up a few things they might need," Ritsuko told her. "All under escort just to be safe. After that they are going to lower the buildings and we'll be on an 'imminent attack' alert."

"So they're expecting something to happen soon?" Maya asked, a tinge of fear evident in her voice.

"We really don't know and that's the problem," she sighed. "The Commander was a total bastard but he wasn't stupid. He had intelligence sources of his own and knew how people thought. He had good reason to believe that SEELE itself would send the 17th Angel against us, very possibly in a human form much like Rei. That could still happen but considering everything that has happened since Yui returned it is also possible that the 17th could be part of the attack Kiel will launch to cause Third Impact. At this point we have no way to know which it might be or if something else entirely could happen. We have to consider any possibility that makes sense and try to be ready when it happens."

"I'm not sure what's scarier," Maya said quietly. "Knowing what's going on around us or being ignorant of it like I was before."

"I'm more scared now than I ever was then," Ritsuko admitted. "When I was helping it along I really didn't care. Whether I helped Gendo or not he was going to make it happen and I felt that I had little reason to want to keep living beyond that point. More accurately I suppose I never spent much time dwelling on the fact that I was helping to bring about humanity's end. But now that I feel I actually have a reason to keep going I'm afraid of that outcome." She rolled her head to the side and looked at Maya. "I have you to thank for that."

"Me?" Maya all but squeaked.

"You care about me as a person, as your friend and not a tool to be used and you care about how I feel." She smiled sadly. "The only other person who was ever close to that was Misato and I was driving her away with all of the secrets. By the time she was taken into the Eva she wasn't trusting me very much and I don't blame her, I wasn't giving her much reason to." She took the girl's hand in hers, making Maya's face light up like a neon sign. She could even feel a bit of heat spread across her own. "You've made me start to feel something other than pain and despair for the first time in a long time and I want to hang on to that."

"S-Sempai...I..."

She squeezed Maya's hand and shook her head. "Later. After all of this is over we can talk about what's beyond this." She smiled, a rare, honest smile. "Besides, I don't think either of us could stay awake long enough right now to have a proper, serious discussion about anything."

As much as she wanted to pursue it Maya knew Ritsuko was right. It was all she could do to keep her eyes open and her ability to think coherently was getting kind of foggy. Although that may have had something to do with the fact that Ritsuko was still holding her hand.

"Right Sempai," she agreed softly with a smile as she followed Ritsuko's lead and settled back into the softness of the couch and closed her eyes. She really hoped that Ritsuko taking her hand meant what she hoped it did, but there were more pressing matters ahead of that, like making sure they actually survived to find out and she would do whatever she possibly could to help get them to that end.

Two hours later when Yui stopped by for a visit she found them still asleep, hands still clasped together between them, a slight, content smile on both of their faces.

* * *

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	27. Chapter 27

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

 **Transposed**

 _ **Chapter 27**_

Mari Makinami, dressed in her school uniform, stood atop the middle most giant solar collector array tower that dominated the Tokyo 3 skyline and fed sunlight down into the Geo-front. It was one of the few structures still above ground since the city had been transformed into battle configuration two days earlier. The few remaining and functional weapons towers and some outlying apartments and houses on the edges of the city were the only other structures that remained above ground. All that was left otherwise was a barren landscape of concrete, asphalt, and steel. It looked lonely and dead and she didn't like it nor the omen that it suggested to her. Good thing she didn't believe in them.

The last few days had been exceedingly busy for her as she repeatedly teleported back and forth over half the world to keep track of things. Kiel, the status of the mass production Evangelions, preparations being made here in Tokyo 3, the placement and hideouts of Kiel's mercenary army. She felt sicker by the day knowing what was out there and what was coming, yet unable to do anything about it unless the advent of Third Impact was imminent. She had appealed once again to her mentor and handler when she made her most recent report and while he sympathized with her plight he told her that she had to stay the course and keep doing what she had been thus far.

It hurt knowing that she was more than capable of stopping all of this herself at any moment but was not allowed to. There were a lot of good people here that could very well die trying to defend this place. Within a matter of a couple of hours she could go and take out the mass production units, she could wipe out all the mercenaries Kiel had hired and she could put an end to that bastard once and for all. No one would have to fight, no one waiting in defence of this place would have to die, and they wouldn't be gnawed at by fear and uncertainty like many of them were now. In particular, Shinji would not have to face any of these things if Gosche would just turn her loose.

She had made sure that she had kept some time available to check on Shinji and she had been surprised by what she saw. While it was obvious that there was still some lingering effects in his demeanour from his ordeal against the 15th Angel, he was doing his best to cope with it and work at improving his skills for the upcoming battle. Besides simulation training in the Eva, he and Rei had been undergoing a crash course in close quarters fighting with members of the SIS. It was pretty much a given that they would face multiple opponents in the MP Eva's, so to give them whatever edge they could to survive they started taking instruction on how to fight up close in either hand to hand combat or with a weapon. Training they should have had long before this.

She had to admit, the SIS people were doing a good job. They were patient, demonstrated and explained every move with Shinji and Rei practising them against each other rather than against someone at least twice their size. They were just beginning to learn after all. With the intel the SIS had gained on the MPE's by capturing two of them in their construction facilities, they could show them were to strike to get the most out of it. It also gave them an idea of what they would potentially be facing. Controlled by a dummy plug, equipped with an artificial S2 engine and wielding bladed weapons with properties of the Lance, they were extremely dangerous and not to be taken lightly. The units would not stop until they were completely incapacitated, or so said the few technicians and scientists that talked when interrogated. The surest way to do that was to destroy the core just as with an Angel, or the Dummy Plug itself. Better yet, destroy both.

She so badly wanted to save him from having to fight that fight. Rei too. She had taken a liking to the blue haired girl. She could relate to the state of her fluctuating emotions because she had undergone something similar after she had been taken out of stasis and stabilized. She had had even less experience with feelings and emotions than Rei had. While Rei had been suppressed by drugs and programming she had been a blank slate starting from nothing. Shinji was good for Rei, he was tolerant and patient with her and really wanted to help her while her presence seemed to soothe his angst and calmed him.

Shinji it seemed was becoming an anchor point for Rei. He seemed to be the person that she put the most trust in and that was something that was going to be very important for her as she recovered from her psychological and pharmaceutical conditioning. Handling the intensity of her newly felt emotions and learning to live as something other than a disposable tool was going to require help and support and despite his own difficulties Shinji would be there for her. However Rei wasn't the only one who was going to need his help.

She had finally gone and checked in on Asuka. While she fully understand what had caused the girl to become so vitriolic and make her behave the way she did toward others, she still found that to be a weak excuse for not at least affording others their basic dignity. It was one thing to snarl and snark and act like others were beneath you, but the way she had treated Shinji was deplorable and had made the redhead one of her least favourite people. The person she had observed talking quietly to Dr. Tokita however was a far cry from the girl she had grown to quickly dislike.

Through the very nature of what she was and through the training and teachings of her mentor, she could literally feel the damage to the girl's soul. She could feel it before her breakdown, great trauma to the mind also affected the soul and left scars upon it. Now it felt like Asuka's soul literally had a hole in it and she couldn't feel anything more than lingering, burnt, ashen traces of the anger and pain that had once been so dominant there. There was still pain there, but it's nature was different. It wasn't tainted with vitriolic pride. It was due to an old wound reopened anew and bleeding that had not been properly tended and infection allowed to fester within it. The wound was clean now but just as raw, certainly larger now after what had happened.

She was vulnerable, a feeling that she would have despised before and never admitted to, angrily rejecting any notion of such a thing or any offer of solace from another. She was no longer burning in a fire of her own creation but was fragile from the damage done and she seemed to realize it. She hated what she had been and feared becoming that thing again. She was afraid and didn't know who she really was.

Mari found herself emphasizing with her to a degree. She had felt the same way when she was revived, although she had no previously existing personality traits, but there was a certain pull from the opposing factors that made up who and what she was. It had been a struggle to find 'herself', to find middle ground to form the personality that was truly her own. Asuka was just beginning that journey. Maybe she could cut her a little slack and when she was sure of her commitment to changing and rebuilding herself she might even offer her some help. It would be unfair to let Shinji carry too much of that burden when he had his own issues to overcome as well.

She knew what it was like to feel overwhelmed and like you didn't matter or were just someone's means to an end, she had been just self aware enough after Kiel created her to know that much. But she had been saved and helped when she could have just as easily been thrown away. She had been shown kindness, love and support, she had been guided gently to find her own way, her own personality and way of thinking and doing things and never forced. But one thing she had never had was a group of friends of her own making. Gosche and the others who helped her were great and she cared for them a great deal, but they were far older than she was.

She wanted to belong with a group of people her own age...or in this case people that she _looked_ to be the same age as and shared a similar mentality with...people she could grow with, have fun with and share experiences with. People who could share each others burdens and help make the weight lighter for each other. In her own way she was lonely and it was hard to see people she had become fond of suffer as they had and not be able to help them. When all of this was over she wanted nothing more than to become friends with them. She desperately hoped that they would accept her and not hate her because she had been forced to stand back and let things happen. But if their hatred and disdain was something she had to bear in the end then she would do so and would have to satisfy herself with the fact that they were still alive. It would be hard and would hurt terribly but that was how things were.

Although, the final acts of this demented play had yet to play out. There was still the possibility that they would die but she had faith that enough things were in their favour now that they would survive. If the need arose she could eradicate the MPE's if the other pilots could not stop them and Kiel would die by her hand no matter what. Third Impact would not happen, that was the one certainty in all of this. The question was though, how much more of a toll would it take before it all came to an end.

She looked up at the clear blue sky above her and took a deep breath. "It won't be long now. One way or another this will all be over very soon."

* * *

 _ **NERV Medical, Psychiatric Ward**_

It was a section of the medical wing that Rei had never entered before, but given the drastic changes going on in her life perhaps it was a place she should become familiar with. She didn't think however that she would be very comfortable talking to a stranger about her life and said stranger would have to have a very high security clearance to even know enough about her to be helpful. As it was the doctor had allowed her to come here without a pre visit like he had demanded of Shinji. Besides, thus far she was managing just by being able to converse with Lilith and Shinji and for now at least that was all she needed.

She was sitting in the waiting area, the same area where Shinji had waited when he had come to visit Asuka. He had expressed some worry when she informed him that she intended to come and visit the Second Child, worry both for her and for Asuka. She understood that he was concerned that she may experience some fear and angst of the girl that had nearly beaten her to death but she had no issues in that regard. If she had not been inclined to allow the Second to do so she was positive that she could have adequately defended herself even if she didn't have the same level of hand to hand combat training that she knew the Second did. He had offered to come with her and while she appreciated his concerns this was something she had to do on her own. It had made her feel good though to know that he was concerned for her.

Her emerging emotions and feelings could be troublesome and confusing, but she had also begun to discover some of the more positive aspects and learn what they meant. For quite some time now she had always had an odd feeling come over her, odd for her at least, when she was around Shinji. It was a dilemma for her and it was a feeling that she didn't experience around anyone else. She felt a warmth and a sense of peace and contentment and it had only become more prominent as the wall built around her by the drugs and her conditioning began to crumble more and more.

The day she regained control of Unit 00 and had the issue with her plug suit had been one of the most trying for her thus far. She had felt a great deal of anger and frustration but it had been Shinji who calmed her and made her feel better. He didn't really know that he had and he had been very upset with himself for his physical reaction to her. She had told him that she didn't mind and that had been the truth. Later however after she had enjoyed a meal made by him in the NERV kitchens and had gotten some much needed sleep, she had spent time in her borrowed quarters in the base's internal housing unit thinking about just why it was that she didn't mind the fact that he had become physically aroused at the sight of her naked body.

She may not have had a great deal of life experience or had a great deal of interaction with others, but she was not stupid. She was well read and studied all manner of subjects beyond the level of her middle school education. The Commander may have wanted an obedient puppet but he didn't want a stupid one. Much of her reading would be considered sterile, text books and such with no allowance for anything written with an ounce of creative thought or imagination to it. Such things may give her ideas counter to his wishes and conditioning.

So she certainly understood the dynamics of why a male may well become aroused at the sight of a naked female. Especially if she just so happened to walk into the shower and request that he peel her out of her skin tight body suit...and _then_ wrap herself around him like a second skin under the soothing hot water of the shower. It had taken her a while to understand that one and just exactly how bold that had been of her. Well to be truthful she had some help there, she had ended up conversing with Lilith and Major Katsuragi while contemplating it. The Major had actually been quite helpful to her even if she had said a number of things that she didn't quite get that she supposed must have been teasing in nature.

The next thing that she found to contemplate was why it was that he reacted that way to her in particular. There were many of other girls her own age who had better physical proportions than herself and who certainly had more outgoing personalities. She had seen many such girls displaying varying levels of interest in Shinji from afar at school, something that for some reason she had felt unsettled about. She had not however asked Shinji why it was that he was interested in her. She knew that he would be quite uncomfortable with that conversation and did not wish to cause him undue discomfort. Lilith and Misato assured her however that he did find her quite attractive and that once he became more comfortable around her and other people in general it would become easier for him to talk about such things.

It may have seemed like a contradiction to that, but she had decided to repeat her actions in the shower from that day. She wanted to know more about not only the emotions she had experienced with him but the physical sensations. Initially she thought she was just seeking understanding but she soon realized that it was just as much because the sensations were pleasurable to her. After each sync test and simulation training session she crossed over into his side of the locker room and joined him in the shower. The first time he was shocked but in all of the subsequent times it seemed like he almost expected it. She had come to realize that as the drugs were slowly being flushed from her system that it wasn't just her feelings and emotions that were changing and becoming more prevalent. She was also experiencing a difference in how things felt physically. Maybe it was because she was now able to associate physical sensations with those emotions and feelings in a way she hadn't been able to before.

What she had felt the day he had accidentally fallen upon her and groped her breast was a far cry from how things felt now. Then, it had left her feeling unsettled even though the contact and the gentle squeezing of her flesh had not been unpleasant. The unsettled feeling came mostly from having never been touched in such a way before. Now, the feeling of so much of their bare flesh being in contact, the feeling of her now more sensitive breasts being pressed against his chest, even the feeling of his erection being pressed against her abdomen felt more than just pleasant. It felt quite good and was even desirable, that was why she had continued to pursue it.

Their physical combat training brought them into a great deal of contact and at times found them in suggestive positions. It was a different but no less desirable feeling. It seemed that she was actually enjoying the physical exertion as well and the shot of adrenaline that it gave her. The feeling of undertaking that exertion with Shinji as her fellow student and sparring partner only added to that. She was getting to feel physical sensations that she had never known before and she quite liked it.

She felt herself blushing as she recalled the previous day and evening. After a good hand to hand training workout she had joined him in the shower once again. As they held each other under the heated spray as they normally did she had found herself moving against him much more than she had before and Shinji had seemed to become more flustered than usual. She finally realized that her motions had been stimulating his usual erection as it was sandwiched between them. She had apologized but had been fascinated when she had stepped back from him and looked down to see said erection sporadically bobbing about on its own. She realized at the same time that it had been rubbing her in a place that was a little lower than usual and she herself was experiencing a new feeling in a place she had never felt it before.

Not knowing quite what it was she had left after a few awkward moments. A couple of minutes later after she had composed herself and resolved to figure this out later she had gone back to apologize for what he must have seen as a rather sudden departure. Knowing his nature she suspected that she may have hurt his feelings or that he was blaming himself for her leaving. When she went back and looked around the corner of the stall she was about to speak but stopped. She was quite fascinated at what she saw. Shinji's face was still flushed as it had been when she left and he was still very much aroused. His right hand was sliding up and down his erection and she could not take her eyes off of the sight.

She wasn't disgusted by it but intrigued, and there was a strange, almost prideful feeling that hit her as she realized that she was the reason for his arousal and the reason why he needed to do something about it. She felt an unexpected heat spread through her lower regions as his pace quickened and she heard him quietly and lustfully call her name. With a grunt he came, expelling what she thought to be a significant amount of semen and she felt a trace of warm moisture trickling down her thighs. She left before he could see her and it took a few moments to calm her breathing and regain her composure once again. It was the first true sense of arousal she had ever felt and it scared her, the feeling was a little too intense for what she could handle at the moment and her mind was too clouded to think properly.

Later in her quarters she began to contemplate those feelings. She didn't asked Lilith or Misato for help, she wanted to understand this herself but they assured her that if she needed them they were there. She was still feeling a certain buzz from her earlier arousal and decided that perhaps those physical sensations were where she needed to start. Standing naked before the bathroom mirror she began to touch and explore her own body. She had read somewhere recently in her quest to expand both her knowledge and the type of things she read that self exploration and understanding the feelings and sensations of one's own body was beneficial. In her case probably doubly so considering the nature of her life up to this point.

It didn't take long to begin feeling sensations similar to what she had felt while both in contact with Shinji and while watching him. Similar, but different. The feel of her hands on her own flesh was much different than the feel of his body against hers but it was still pleasurable. It had also been quite easy to lose her rational thought within that pleasure, her immediate observations being lost to the idea of how it would feel if Shinji were touching her this way and how it would feel if she were to do the same for him. She was intrigued by both ideas.

When she came her legs nearly gave out on her, causing her to lean on the sink for support and eventually she had little choice but to let herself sink to the floor. The feeling was indescribable but it was also frightening in its intensity. Despite that she knew it was something she wanted to feel again. It was like every nerve in her body had come alive, a far cry from the dull, thick, muted sensations that made up most of her life. The only thing comparable to this was the intense pain she had undergone on occasion but she certainly had no desire to relive any of those instances.

She looked down at her hands, currently covered by the material of her new plug suit. Since they were on a state of constant alert she thought it wise to wear it, though it did prompt her to think about having Shinji peel it off of her again. She wondered if perhaps she was becoming a pervert, but that was something to be contemplated at another time. After last night she felt physically different yet again, or at least she was perceiving herself differently on a physical level once again. Thankfully the physical differences in her were far easier to comprehend and cope with than the mental and emotional ones were.

She wondered if she would react differently than she anticipated she would when she saw the Second Child. She did not fear her assailant, that she was sure of, but she doubted that what had been her automatic sense of apathy would be how she felt or reacted now. Truthfully she had no more idea what to expect her own reaction would be than she did Soryu's. The Second might not even wish to see her and quite frankly she wasn't entirely sure of what she was going to say to her if she did. For whatever reason she had felt that she needed to come here but had no clear reason in mind as to why or any real idea of what she would say. Given her current state that wasn't altogether surprising. Perhaps this had not been the best of ideas.

Fate didn't give her a choice however as she heard a noise and looked up to see Asuka and Doctor Tokita entering the waiting area. The Second Child looked rather frail to her in her white hospital pyjamas and with bandages on her hands and a walking boot surrounding her right foot and ankle. She looked thinner than she recalled as well and there seemed to be something off about her. Her posture and the way she shuffled into the area showed a definite lack of the overconfidence and brashness that she was used to seeing in the girl. Now she looked slump shouldered and defeated, almost timid. Her body language suggested that she was afraid. When Asuka finally looked up everything that she had observed about her was reflected in her eyes. It was clear that for better or worse the Second Child was greatly diminished and not who she once was.

"Pilot Soryu," she said in her usual flat and quiet tone. Unless she was seeing things it seemed that the Second actually flinched at the sound of her voice.

"Ay-Ayanami," she stuttered quietly, not sounding anything like her usual self. While her head was up her eyes were still downcast and she could not look her in the eye. Rei found that some small part of her was irked by this, finding it unacceptable. However it wasn't as if she could cast recriminations at the redhead, she had allowed her to nearly beat her to death after all and shared some part of the blame.

There was a hitch in Asuka's breathing and she began to shake. Tears streamed down her face. "I'm sorry," she rasped. "I'm sorry."

"It was not you." she deadpanned.

"It was!" Asuka cried. "I hurt hurt you. I t-tried to kill you!"

"I see you standing in front of me but I do not see the person who harmed me," Rei pressed. "I allowed that person to beat me. I did not defend myself. You are not that person."

"Why?" Asuka pleaded brokenly. "Why didn't you fight back?"

"At that time the purpose for which the Commander required me was no longer necessary," she said. "I had received no further orders or direction. I had nothing left, no reason or requirement to continue."

"I...don't understand," Asuka said as she tried to regain her composure.

"NERV has a great many secrets that only a very few are aware of," Rei began. "Things that your old self would have never believed about the organization she so proudly served and defended from criticism." She looked Asuka unflinchingly in the eyes. "I am both one of the few who know those secrets and one of the secrets itself. NERV's foundation is built upon secrets and lies."

"None of which she needs to hear at this time," Dr. Tokita cautioned.

"I am aware of this and have no intention of revealing any unless it is required," Rei said, shifting her attention to the doctor for a moment before turning back to Asuka. "Which is why my answer to you is vague and does not fully explain my motivations."

"Why did you come here Ayanami?" Asuka asked, unable to continue meeting Rei's gaze. "We were never friends and I treated you just as poorly as I did Shinji."

Rei regarded her for a moment. "I have been undergoing a great deal of change lately, seeing the world, those in it, and my own place in it differently than I ever had before. I spoke with Shinji after he visited you. I believe the reason that I came here was to show you that I have recovered and have no ill effects and that I do not bear you any malice for what happened."

"How can you not after what I did to you?!"

"Why should I be angry over something I could have stopped but did not?" Rei countered. "Any anger I feel is because of this, we have caused Shinji to worry about us both and left him to fight the Angels alone. I am just as much to blame for that."

Further conversation was ended with the sound of shattering glass as the windows separating the waiting area from the greenery outside came apart under a hail of gunfire. Rei grabbed Asuka and pulled her down to the floor with her. Dr. Tokita landed next them with a grunt of pain, the left sleeve of his doctor's coat stained red from a wound to his arm. Lifting her head slightly she saw four heavily armed men dressed in forest camouflage and their faces painted to match approaching the now shattered windows. The thought struck her that with the way they were dressed and since the alert sirens hadn't gone off that these men had already been inside the Geo-front. If she was right they were either spies that had escaped the SIS purge or they had found a way in undetected and had been hiding in the forest.

The men entered through the empty window frames and fanned out before them, keeping their guns aimed directly at them.

"Looks like luck is on our side boys," a tall light skinned man with several days worth of stubble on his face said. "Two of the three pilots right off the bat."

A moment later the alert sirens began to sound throughout the base.

* * *

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	28. Chapter 28

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

Back when the OC's I'm using first appeared , I warned that they would appear again. After Gendo got his deserved reward I got an anonymous review from a troll crying that I had ruined the story by having the OC's take over.

Poor stupid troll, evidently he has never actually read a story where the OC's really did take over. (Had other trolls actually questioning my characterizations early on. Too bad they were so mesmerized by the bright colours and big explosions when they watched the series that they paid no attention to the characters themselves and had no clue what they were bitching about)

So to all the trolls, here's a hearty screw you, and I will continue to otherwise ignore you for being the waste of genetic materials that you are...all while a couple of my friends on the site here and I continue to laugh at the ridiculousness and total inaccuracy of your reviews when I share them with them.

With that said, the OC's will be playing a prominent role over the next couple of chapters and then again close to the end. If you don't like that then go read something else and save your complaints for someone who actually cares. Valid questions and true constructive criticism I accept, stupidity I don't since I have a very low tolerance for fools.

If you are okay with it, then read and enjoy. It's been a while since I wrote action scenes but I think they came out alright.

 **Transposed**

 _ **Chapter 28**_

 _ **NERV Recreation Deck**_

Until his lessons with Misato and Lilith and his time spent floating with Rei in her mindscape, Shinji had never given much thought to swimming. Up until then he had been convinced that humans were not meant to float and had done his best to avoid the water. However since those two happenings he had grown to rather enjoy it. Over the last week he'd had the opportunity to swim here with Rei during breaks in their training and he had really enjoyed it. And he could not deny that she looked really good in the two tone blue, one piece racing suit she wore. Though he strongly suspected that she would rather swim in the nude.

As such, as he swam he found himself thinking about how things had been with Rei recently. With their training they had been spending a great deal of time around each other and with their hand to hand training in particular there had been a great deal of physical contact between them. Not to mention her forays into the shower with him which Misato just could not restrain herself from mercilessly teasing him about, as if her commentary about Rei's bathing suit weren't enough. Not to mention her explanation as to what kind of bathing suit _she_ would wear. Her descriptions alone damn near gave him a nosebleed.

The first time Rei joined him in the shower he had chalked it up to her seeming lack of care about modesty and propriety and she _had_ needed his help to get out of her plug suit. The second time was pretty much as shocking as the first. All she had really said was that the hug, and their naked contact in general, was both pleasant and desirable. Her straightforward and bold curiosity was sledgehammer like when explained in her quiet manner of speaking. The two things were so much of an opposite. By the third or fourth time he just kind of stopped thinking so much about it and almost expected it from then on. He was ever so slowly getting used to all of that intimate contact and was realizing that it was actually kind of nice. If only he could do something about becoming so aroused by it. Damn late blooming teen hormones.

He was somewhat blown away by her when they first swam together. He was still very new to it and was slow and steady as he gained confidence, but Rei swam like she belonged in the water. He supposed that wasn't far from the truth really. She had begun life floating in liquid, even if it wasn't water, and had spent a great deal of time floating in a tube of LCL as her memories and experiences were downloaded for the dummy plugs. Water or liquid was probably as much or more of a natural environment for her than it was for any one else on the planet and watching the way she moved and cut through the water was something that amazed him.

He stopped his laps and just let himself float in the middle of the pool, wondering how it was going with her visit to Asuka. It was kind of hard for him to understand how Rei was neither angry with Asuka over what she had done nor fearful because of it. Even with her evolving emotional state she seemed rather neutral about it. Rei's situation was so unique that he supposed it wasn't strange for him to not be able to comprehend it. Based upon his own visit he knew Asuka was going to be nervous and afraid and probably expecting the same kind of reactions he had thought Rei would have. One thing that they both had in common right now was a struggle with who they really were.

In his own way he supposed that he was struggling with the same thing himself. He was not the same person he was when he first arrived in Tokyo 3, not even the same as he was just a few weeks ago before his mother came out of Unit 01's core and he began to learn the truth of what was really going on. His ordeal against the 15th Angel had changed him yet again and had seemed to make things even more confusing for him. Confronted once again by the familiar pains of his own life, confronted with the pains and the terror of Misato's life as if all those memories and experiences were his own, and the revelation of how they both truly felt about each other. That fact that he had strong feelings for several of the females in his life when he had been afraid to even contemplate his feelings for even just one of them.

He felt a little like he was being tossed around in a typhoon and he had no idea where he was going to land let alone if he was going to survive the landing. Having his mother back, interacting more with Rei and with Misato, even if it was just in his head right now for the most part, these were all _good_ things but he was afraid that at any moment he would discover it was all a lie and everything would come crashing down around him. That old self loathing and lack of confidence was a hard thing to escape, especially when you had known little else for most of your life.

As it was he knew he was barely holding himself together. In a short period of time so much had happened and none of it had been small and insignificant. The return of his mother had given his life and his abused psyche a much needed second wind, a bit of a reset that allowed him to pull himself together a little bit. Even through the truths revealed to him by his mother and Sub-Commander Fuyutsuki he had kept it together. It was both equal parts terrifying and as he had recently figured out, oddly settling. Certain truths had given him answers he had needed, others gave him a much needed perspective on what was going on and why. As terrible as some truths were, knowing them had forced him to think instead of react hysterically or in ways that would only further damage him.

Then there was discovering the truth of how he really felt for some of the people around him, principally Misato, Lilith and Rei. As for Asuka, it was like she was an entirely different person now, one he barely knew but it was still encouraging that she seemed inclined to want to get along now that the angry side of her seemed to be gone. Again, as with the other revelations this too was a double edged sword for him. He was grateful to know how they felt about him, that those feelings synced with his own rather than being in opposition to them. He had thought that he was someone who was incapable of being loved but they were proving him wrong and it was going a long way to keeping him together.

That didn't mean that he still wasn't close to being overwhelmed and that he wasn't still scared half to death. The ordeal with the Fifteenth had nearly destroyed him and if it hadn't been for Misato and Lilith and later Rei, he would have completely lost himself to the pain and agony that has permeated his soul. He could still feel it, he still wasn't right or even the same as he had been before that ordeal and it was the constant reassurance of Lilith and Misato in his head, the closeness and support of his mother, and his increased interactions with Rei that were keeping him upright and moving. In all of them he had found new reasons and strength to keep going and he had a growing determination to do just that and see this all through to the end so that they could all finally know peace. Still, it was a struggle and wasn't easy. He supposed nothing ever truly worth anything ever was.

The sound of the alert sirens going off startled him, causing him to thrash about and end up under water. He came up coughing and spitting but immediately made his was to the side and climbed out. He had kept his clothes and his plug suit ready at a poolside table rather than inside the pool complex change rooms in case he needed to change quickly. He was halfway into his plug suit when the main door opened. A man dressed in the tan uniform of NERV's internal security staff stepped in, pistol in hand. A feeling of dread landed in the pit of his stomach. There was only one person who should be coming through that door to get him and it wasn't this guy.

"Well, that was almost too easy," the guy said through a sneering grin.

"You're right, it was," a woman's voice said, right before a pair of hands grabbed the guy around the head and face and violently yanked him back out the door.

A lot of people would have balked at playing bodyguard while someone swam at the pool, but Melissa Lake didn't mind. Ever since the base and the city had went into battle configuration and lock down members of the SIS team had taken turns shadowing the pilots and senior staff and today was her turn to shadow Shinji. She found him to be a pleasant young man and she had enjoyed being a part of his training team, but he did make her think of the little brother she had lost and that was always a painful thing for her.

She knew Shinji was looking for some quiet time to swim and think so she left him to it and patrolled the hallways between the main entrance and the entrances on the far side of the pool complex that led to and from the change rooms. As required, just in case, she was dressed in her full battle gear. Combat vest, her two pistols, one strapped to either thigh, a knife across the small of her back, her HK 416 A5 in hand and extra ammo clips scattered about her person wherever she could secure them. A tactical radio was in a chest pouch on her vest and the earpiece was secured in her left ear. She had been about halfway back to the main entrance when she heard a quiet call over her tactical radio from her partner.

"Zero-Three...Snake Eyes."

Zero-Three was his call sign, hers being Zero-Two. Snake Eyes was the alert code for hostiles in the area. They had hostiles in the hospital ward. She took off for the main entrance to the pool and just before she got there the alert sirens went off. In her ear she heard a report from up top that the armoured unit of the Japanese military that had been sent help them out and form a perimeter around the base had turned the turrets on their tanks towards the entrances and opened fire.

She slowed at the corner in the hall just before the doors to the pool. Peeking around she saw a tan uniformed NERV internal security agent enter the door.

"Well, that was almost too easy," he said to Shinji, his pistol more or less pointed in the Third Child's direction. Slinging her rifle over her back, she crept up on him while he was distracted.

"You're right, it was," she told him as she grabbed him around the head and face and yanked him back out the door. She pivoted and threw him down, the pistol flying from his hand and clattering across the floor. She immediately came down on him with her right knee between his shoulder blades. Grabbing him by the chin with both hands she yanked back sharply and to one side. There was a sickening snap-crunch and the man went still.

"Zero-Two," she called into her radio. "Found a rat at the pool. Took care of it. No damage on our end. We'll be making our way to the cages now."

"Zero-One roger that," Colonel McKinnley answered. "Attacks suggest that we have had hostiles hiding in the Geo-front waiting."

"Copy that," she responded as she picked up the rat's gun and dropped it in the trash can by the door. Unslinging her carbine she let the assault weapon lead the way she kicked the door open and scanned the area. All she saw was a startled Shinji halfway dressed in his plug suit.

"I appreciate the show Shinji but you're a little young for me and now isn't the time." she said with a smirk. She just couldn't resist.

"Gah!" he exclaimed as he turned red and hurriedly finished donning the suit. "S-Sorry."

She waved off his concerns. "Not the first time I've been flashed," she grinned.

"H-has the attack really started?" he asked nervously.

"Afraid so," she confirmed. "But don't worry Shinji, we're not unprepared and we have some people here defending that are really good at what they do. Stick close to me and I'll get you where you need to be and Matt will do the same for Rei and Asuka. You can count us, we won't fail you."

The conviction that he saw in her vivid blue eyes was absolute. The type of conviction that didn't suggest that she thought they would win this fight, but that she _knew_ they would and that there was no other possible outcome. Even as nervous and scared as he was he couldn't help but want to believe it too.

"We'll do the same Captain Lake," he said bravely. "We won't let you down either."

"That's the spirit Shinji," she smiled. "And call me Mel, we're friends and comrades in arms here after all. Now, let's go kick some ass and put an end to this shit."

With a resolve he didn't know he had he readily followed her out the door and into whatever awaited.

* * *

 _ **NERV Medical, Psychiatric Ward**_

Matt Riker was just down the hall from the visitors area in order to give them their privacy. He could keep an easy eye on the area by checking the convex mirror affixed to the ceiling at the intersecting hallway in front of the nurse's station just beyond the visitor area. The moment he heard the windows being shot out he took a peek around the corner and saw everyone hitting the floor. Pulling back and keeping his eye on the mirror he keyed his radio.

"Zero-Three, Snake Eyes." Flipping the safety off on his Benelli M5 shotgun, he looked up at the mirror again and waited until he saw the overconfident shooters step in.

"Look's like luck is on our side boys," he heard one of the men say. "Two of the three pilots right off the bat."

The response the guy got was a large blur stepping around the corner and firing a 12 gauge round of '00' buckshot into his face and neck. They were caught flat footed and the quick boom-boom-boom of three more shots took the rest of them down.

"Stay down!" he yelled as he passed the two girls and the doctor, keeping the shotgun trained on the enemy and taking quick glances outside to make sure no more hostiles were about to show themselves. The men he shot were down for the count, but all the same he disarmed them and tossed the weapons outside the shattered windows. Sidearms were a mix denoted by personal taste but the assault rifles they carried were Sig 716's, all looking close to new. He paused to take another look around but didn't see any signs of anyone else in the area. Until he looked up. He grinned.

"She owes me fifty bucks," he smirked. "I told her someone would try it."

Above and away from the side of the NERV pyramid where he was, he saw at least half a dozen parachutists gliding down and more or less toward him. He keyed his radio. "Zero-Three, we have para's." They had either jumped from one of the buildings hanging from the ceiling or somewhere up in the roof structure.

"Zero-Nine, we see them."

He picked up one of the discarded Sig's, flipped the fire selector to single shot and banged through the thirty round magazine at the ones closest to him. He tagged one for sure and possibly a second, it was hard to tell at this distance. Finished, he dropped the rifle and went back inside, reloading his shotgun from a pouch of shells on his hip.

"Everyone all right?" he asked.

"We are fine," Rei answered, getting to her feet and pulling Asuka up with her. "But Dr. Tokita has been wounded."

"It's not serious," the doctor said as he stood and removed his coat to inspect the wound. "A deep graze. I had worse in training." Riker raised an eyebrow. "I spent four years in the Army to help pay for my education."

Riker nodded. "You have a safe spot for you and the remaining hospital staff?"

"We have a storage room set up along a monitored hallway," the doctor answered. "I can access the security cameras there with my phone."

"Good," Riker said. "Feel free to help yourself to the discarded weapons, just in case. These ladies and I have someplace we need to be."

"Right," Tokita responded. "Good luck to you."

"And you doctor." With that they separated, Riker and the pilots going up the hallway where he had been waiting before the shooting started.

"Where are we going?" Asuka asked.

"To the Eva's," Rei answered as she helped the other girl along as she hobbled on her booted, broken foot.

"B-but I don't know if I can still pilot," she stammered.

"If you cannot then at least you will be safe from these invaders," Rei told her. "The pilots are one of their primary targets."

"What?" But why?" This was making no sense to her. Who would be invading the base and why were the pilots being targeted? Why would other humans attack the one place that was their best and nearly only defence against the Angels?

The man leading them stopped and turned to look down at her. She suddenly realized just how big and thus intimidating he was. "I know you have questions and that this is all very confusing," he began. "Believe me, I get that. But we really don't have time right now for a lesson in history or current events. The short hard version is this. NERV is controlled by a group called SEELE. SEELE's goal has always been to create a Third Impact under their own control for some hair brained idea of kicking what they see as mankind's stagnant evolution in the ass and turning us all into one big blob of souls that approximates a higher being free of the pains of our human lives." He wasn't about to drop the truth about Kiel and mankind's origins on her. What he had said was probably too much already but they didn't have time to tell the whole story anyway. "And free of any of the good stuff either," he continued. "It's shit and it's stupid but there it is. Bottom line, we win or else, just as it was when fighting the Angels."

"They have seven mass production Evangelion units at their disposal and possibly the 17th Angel," Rei added, dropping another few tons of TNT on the poor girl. "Shinji and I will fight them. If you can pilot your help would be appreciated. If not, you will be safe within Unit 02."

Evidently even that small amount of information was a little much for Asuka to handle right now. She was shaking and her mouth opened and closed like a fish gasping for air. That short explanation had just turned on its head everything she had known and believed when it came to her role as a pilot for NERV. Worse, she knew that it wasn't then entire story. She wasn't stupid.

"Okay, take a minute to calm down," he said. He could give her that much, as little as it was. "I need to take a look up ahead anyway but we can't delay for long."

He pulled the 9mm HK USP from the holster strapped to his right thigh and handed it to Rei. She had a rudimentary knowledge of how to handle a gun prior to the recent training she and Shinji underwent and she become fairly proficient in short order under his tutelage and was willing to carry and use a gun if the need arose.

"If we get separated or you see something not friendly coming up on us don't be afraid to use it," he told her.

She nodded and he pulled a spare magazine from a slotted pouch on the right side of his vest and handed it to her. She looked at it for a moment before unzipping her plug suit and stuffing it between her breasts.

"I have no pockets," she said simply.

He blinked. "Should of thought of that. Nice improvised solution though." He grinned. "Maybe I should suggest that to Mel as an extra place to carry more ammo."

"She would throw something at you and call you bad names," Rei deadpanned, having seen the battle partners interact. It had been fascinating as well as entertaining.

"Yeah, she probably would," he agreed. "Totally worth it though." He turned serious again. "Hold tight here, I'm going to go check the next hallway."

As he left he heard Asuka quietly and shakily asking who he was. In all of the excitement he hadn't introduced himself, but a little lost etiquette was the least of their worries and Rei could fill her in while he checked ahead. He would have to trust the quiet girl to keep Asuka moving, not fair he realized since Ayanami had baggage enough of her own and Asuka was already a big bag of uncertainty even without the quick rundown he had given her. But, she needed to know at least a little of the truth, enough to let her know that this was a serious situation. As serious or even more so than any of the Angel attacks. She also deserved to know as someone who had been an active combatant in all of this. Too bad the timing royally sucked ass.

The doors at the end of the hall, like all doors in this ward, were electronically locked at all times with entry and exit being gained by being buzzed in from the nurse's station and reception area or with an access card. He had been given a card just as all of the SIS people on site had that gave them access to any location in the base. His plan was to get them from here to the ICU ward where Ayanami had been kept when recovering from Asuka's beating and take the emergency elevator there that led directly to the Evangelion cages. To get there they had to go through these doors and hang a right, go down that hall past two more intersecting hallways and then go left and proceed down a long corridor with one connecting hall on the right. Problem was it was entirely possible that there would be hostiles elsewhere in the hospital complex. He doubted that the ones he had already dealt with would be all.

The doors each had a small steel mesh reinforced window in them which would afford him little visibility into the hallway without sticking his face right in front of one of them, which he wasn't about to do. As it was he kept his eyes on the windows as he crossed to the right side of the hall, the reader for the security card was situated on the wall just beyond the swing reach of the right door when it opened. He stopped and listened for a moment before sliding the card through the reader and quickly taking a few steps back along the wall.

The doors swung inward automatically and were halfway open when a burst of gunfire chewed into the right hand door. He went into a crouch with his shotgun ready to take out anyone who showed themselves. A hand holding a pistol appeared around the corner, firing immediately. It spit out two rounds that struck the wall above and well behind him before he fired. The gunner screamed as his pistol and part of his hand were blown away along with a chunk of the corner in a splash of blood and plaster dust.

He stood and charged the door, firing another round out into the hall to keep their heads down. Whipping to his left he took in the scene in an instant. The wounded man was on the floor just around the corner, screaming and clutching his mangled hand. Two men were stacked up behind him along the wall and a fourth was directly opposite them across the hall. In the natural course of his pivoting turn he fired at the guy across the hall first, his head exploding like an overripe melon. The weapons held by the other two were coming up on target when he fired again, over rotating a bit and having the mass of buckshot slam into the wall right next to the first guy's face. Half the shot sent up a shower of plaster dust and debris, the other half took out the right side of his face.

Screaming, he was launched back into the guy behind him who had been trying to step around him to get a clear shot. Stumbling, he had no hope of saving himself as he was left wide open, a shot to the chest pulverizing his heart and lungs and slamming him to the floor. A quick look up and down the hall showed him no more immediate threats. The guy with the mangled hand was clawing at the sub machine gun that was slung over his chest, all while cursing at him in a mixture of English and some language he didn't understand. Holding the shotgun up and away in his left hand, he drew the .45 from under his arm with his right and put a bullet through the man's head. Shifting his aim he put the other wounded man out of his misery as well.

Holstering the pistol he moved back to the doors. "Heads up Ayanami!" he called out.

He peeked around the corner to see her down on one knee and aiming his pistol down the hall toward him. Asuka was crouched close behind her. Seeing things were alright he came around the corner, reloading the shotgun as he went. They stood and and met him halfway.

"Seems like they've made a concerted effort to gain entry through the ground floor here so we're bound to run into more of them," he said. "Not too surprising since it is a weak point but we thought we had accounted for it better than this." He looked to the redhead. "You doing okay Asuka?"

She nodded hesitantly. "I-I think I'll be alright. I don't get any of this, but like you said, we don't have time right now." It looked like her military training from her time in NERV Berlin was kicking in, as sick as it sounded for a fourteen year old girl to have to rely on that.

He gave her a slight smile and a nod. "Good. You stick close to Ayanami and both of you stick close to me. We'll get there safe and sound."

"What about Shinji?" she asked worriedly.

"He's with my partner so he's in good hands," he assured her. He went to his radio. "Zero-Three, ran into a few more hostiles but we're on the move now."

"Any damage Zero-Three?" the Colonel asked.

"Negative," he responded. "But it looks like they planned multiple entries to this level. They way they're dressed tells me they may have been camped out in the Geo-front forests."

"Affirmative Zero-Three," the Colonel said. "We have reports of multiple entries all around the ground level of the pyramid. It's looking like most of our raiders were already inside or coming from the hidden entrances we were worried about. Very few seem to have been coming in from topside. I'm trying to direct as many resources to the pyramid as I can."

"If they show tell them to holler loud," he said. "I'm shooting first until we reach the cages."

"Roger that Zero-Three. At the moment anything you run across will be hostile. Your tracker is the only friendly in hospital wing."

Each SIS member had a tracker on them that the MAGI could track around the base. "Roger. Moving out." He turned to his charges. "Alright ladies, lets go."

* * *

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	29. Chapter 29

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

 **Transposed**

 _ **Chapter 29**_

The recreation centre complex where the swimming pool was located was on the opposite side from the hospital in the huge pyramid that made up the outwardly visible part of NERV's base inside the Geo-front. It too was on the ground floor and it was evident by the sounds of combat echoing through the halls that somewhere beyond their position hostiles had gotten in here as well. They hadn't gotten far up the hall from the pool when they began to hear it.

If the enemy could gain access this easily into the Geo-front then all of the work they had done to block or redirect access from up top through the city had been a mostly wasted effort. They knew it was a very real possibility that SEELE had a number of ways in that didn't show up on any set of plans for the place, but judging by the amount of activity she was hearing over her radio those ways in were either numerous or so well concealed that no one had ever found even a trace of them in all of the time this place had been operating.

It was just as likely that no one had ever even bothered looking. It wouldn't have surprised her if Ikari had known, but even if he didn't know exactly where they were it wouldn't have mattered to him anyway. He would have just used the attack to cover his move to take Ayanami down into the depths of Terminal Dogma and begin initiating his version of Third Impact. She supposed that with how long Kiel had been planning this that he certainly would have factored in needing undetectable ways into the place, but it was still mind boggling to think of the sheer amount of detailed planning that must have gone into this entire thing. If only he had used that intellect and attention to details to do something good and worthwhile.

The preferred and most direct route for her to get Shinji down to the Eva cages was to head for the main entrance and reception hall of the pyramid and to the central bank of elevators there, but it seemed that the enemy was already ahead of her. She _had_ factored that into her list of possibilities and it seemed she was now going to have to deviate and head for her secondary choice already. There was a set of utility elevators in this end of the building that were near a maintenance and storage area. The enemy would probably try getting in there too but she hoped to slip by them by getting to a set of maintenance stairs and going down a flight or two before trying for one of the elevators there.

She stopped them at the first main intersecting hallway they came to and motioned for Shinji to stay behind her. She knew he could hear the fighting up ahead just as easily as she could and the poor kid had to be rattled by it, yet it seemed he was coping with it remarkably well.

"Looks like we have to take a detour already," she told him. She listened carefully to try and determine if any of the fighting was taking place down the corridors to her left and right. She thought she heard faint sounds in the distance down to her right and nothing to the left, but it wasn't easy to say for sure with the commotion further up the hallway ahead of them.

She let out a breath and took a quick look left and right before quickly pulling back behind the corner. She hadn't seen anything and no one had tried to blow her head off. She took a second, longer look, mostly concentrating on the right hand hallway. There didn't seem to be any imminent danger from that direction.

"Okay Shinji," she said. "We're going left. Ready?" The boy nodded. She could see the fear and nervousness in his face and in his posture but she could also see enough resolve in his eyes to know that he wasn't about to run or hide.

She rounded the corner with him right on her heels and they paced a quick walk/slow trot up the left side of the long hallway. A little over a hundred feet up ahead of them was a hall that went to the right. When they were thirty feet from it someone peered around the corner and quickly pulled back. She pulled Shinji across to the other side of the hall with her and steered him down to the floor. It was good timing. The person whipped around the corner almost immediately and opened fire on where they would have been if they had kept to that side. Realizing they had crossed the hall he was sweeping his fire towards them when she opened up his chest with a three round burst, sending him sprawling across the end of the hallway.

As she fired a couple of more bursts into the wall above the dead man to keep any friends he had with him at bay for a moment, she noted that he was garbed in forest green camouflage like the one's Matt had reported running into. She motioned for Shinji to stay down where he was and she quietly crept towards the corner. She could almost feel that there was at least one more hostile around the corner and she had long ago learned to trust her instincts. She wasn't about to make a juicy target of herself to find out and if he wasn't either then she needed to do something to at least distract him for a second in order to make a move.

Looking down she saw a shell casing near her boot that had rolled a few feet down the hall from the man she had shot. An idea crossed her mind, one that relied on basic involuntary reactions. It was worth a shot. She picked up the casing and when she was a couple of feet from the corner she tossed it into the adjoining hallway, at an upward angle so it would hit the ceiling. As soon as it left her hand she took a couple of quick steps and hit the floor, sliding across the opening on her left hip and shoulder. There was indeed a another man standing around the corner and the tossed shell casing had indeed done as she had hoped. It caught his attention just enough to make him to avert his eyes to it for just a split second. It was enough. As his eyes snapped back to her she was already pulling the trigger, pounding two three round bursts into his abdomen and chest.

Truthfully, she couldn't believe that it worked, but she'd take whatever lucky gifts she could get. She didn't have time to wonder about much as she heard heavy boots slapping the floor from well down the same hallway, followed immediately by the sound of rifle fire and bullets slapping into the wall above and behind her. Luckily for her the shooter's aim wasn't great as he fired while running. She returned fire, sending three round bursts down the hall. She felt something tug across her vest over her right shoulder and heard the bullet whiz past her ear, while at the same moment her foe was hit and went to the floor. As he cursed and screamed in German and writhed on the floor she realized that unlike the other two, he was wearing a vest.

She didn't know if her tri burst had perforated the body armour or just slammed into him hard enough to break some ribs and knock the wind out of him but she wasn't going to wait ti find out. Quickly getting to her feet to get a better angle as he struggled to get up, she sent more rounds downrange, finally drilling him in the head. Keeping a hard eye on things down the hall to make sure no one else appeared, she swiftly and smoothly swapped the empty magazine in her carbine for a fresh one. She didn't bother checking the graze on the shoulder of her vest.

"It's all clear Shinji," she called. She could see him shaking as he stood up. She couldn't blame him for being rattled by the close gunfire. As he approached her she made sure to keep herself between him and the sight of the dead mercenaries. Draping an arm over his shoulder she steered him by the carnage and up the hall. "I know it's tough by stay with me Shinji. You can do it."

"H-how do you do it?" he asked. "How do you fight against guys like this all the time?"

She gave his shoulder a squeeze. "Same way you do Shinji when fighting the Angels. Someone has to do it and I can."

* * *

 _ **NERV Command Deck**_

Just as with most days recently, the morning started with a certain air of tension on the command deck. The _'Bridge Bunnies'_ , as they were collectively know were busy at their usual assigned tasks of monitoring the base functions, the defence grid, or what was left of it, and watching the scanning systems for not only Angels but anything else that might potentially be hostile. Ever since the city had been shifted to battle configuration the SIS people had been busy setting up their command centre in Gendo's old office. There wasn't room for them and the NERV personnel here on the command deck, and once the action started there would be too much noise from each groups respective comm systems and duties for any of them to work effectively. Currently, Colonel McKinnley, Sub Commander Fuyutsuki and Kaji were in the command staff's observation post above them. Yui was there as well speaking with both of them.

Ritsuko was feeling that tension as she took her freshly poured cup of coffee to the bridge station she was using and watched the activity around her. As they had for days, both the NERV and SIS people were used to operating under stressful conditions and to their credit they all were going about their work efficiently and calmly. While she couldn't say much in her observations of the SIS people since she really didn't know any of them, her own people she did know and she could see the subtle hints of the strain they must be feeling. The impending appearance at some point of seven mass produced Eva units was daunting enough with the spectre that the Seventeenth Angel might arrive with them. Never mind that it could well coincide with a human attack on the base.

In relative terms, the Angels were a known quantity even in their variety and unpredictability. But seven mass produced Evangelions, all piloted by a dummy plug system was something that seemed far scarier somehow, maybe because they were monsters that had been crafted by human hands rather than being some form of invading alien. They all remembered the relentless savagery that Unit 01's dummy plug had displayed as it tore the possessed Unit 03 to bloody chunks. The idea of something like that being repeated and multiplied by seven was not something they wanted to see and it was hard to keep one's morale up under the shadow of that potential eventuality. Yet even with that hanging over them they were still able to do their jobs. They had been offered the chance to evacuate if they wished but they stayed in spite of it.

She was feeling the fear herself with an added layer of guilt. While she certainly wasn't the only scientist within NERV and SEELE to have worked on the dummy plug project, her work certainly had contributed to the whole. As it was she had been trying to find a way to atone for that but without having access to the programming for the mass productions units she had little hope of doing anything to disrupt the connection between the dummy plug and the unit. Sadly, as always, they would have to rely on their own pilots to handle them. Their plight was something else that had tacked itself onto the cloak of guilt she wore and weighed on her conscience the closer they got to the end of things.

She had treated all of them, and Rei in particular, as little more than mere parts of the Evangelion. She had long tried to tell herself that investing any emotions in them was a fools game and her detachment was far better than Misato's close involvement. Her friend's torment was her example to justify her way of thinking. Misato put herself through hell being caught between her obsession to kill the Angels at all cost and the need to use children to do it. Despite her military training and the fact that she was their commanding officer it was impossible for her to stay at arms length from them. She had already known Asuka, took an instant liking to and had an instant connection to Shinji, and if it wasn't for Gendo's tight control over Rei she had little doubt Misato would have been much closer to her as well.

But her, she had been completely detached from the them and perfectly alright with using children as soldiers and to let them suffer for what was ultimately to be a pointless cause. By the hand of the Angels, by Gendo, or by SEELE, the world and in particular mankind was supposed to come to an end. No matter what those children did it had all been designed to be for naught. Save the world from one threat so it can be destroyed by another and she had been right up to her neck in helping to make that happen.

She looked to Maya and once again thanked whatever lucky star that had deigned to pass overhead and gift her with someone who supported her and believed in her despite all that she had done. She was the ray of light that illuminated her way out of the darkness and the lifeline that kept her from drowning in guilt, loneliness, and misery. Maya was making her feel like a human being again instead of a monster and returning a little bit of hope to her life. One way or the other they were close to the end of this fifteen year nightmare and she could only hope they came out on the positive side of it. She had reasons to actually want to now.

"Colonel!" she heard one of his comm techs call to him on the radio he carried. "Topside is reporting that the JSDF armoured units outside the main entrance are turning their turrets on them and opening fire."

"Damn it!" he cursed. Evidently the help he had been assured was reliable was anything but. "Sound the alert and get me General Nakamura on the line, he's got some explaining to do." He turned and headed for his command post but before he left she also heard the reports of hostiles in the hospital and recreation wings.

"Get ready," Fuyutsuki told his own people. "We could be seeing incoming Evangelions at any moment."

"Sempai, it's starting," Maya called.

"I see it," Ritsuko acknowledged. "When they hit that firewall start sending out every surprise we have. I'm activating our mole programs. All of the other MAGI should be connected together for this and focusing on attack right now. Our viruses should spread through all of their systems in a matter of seconds."

With a flurry of keystrokes she sent the commands to awaken the digital monsters they had left in NERV 01's MAGI. As it was, the virus would have been leaving pieces of itself throughout their systems since she originally planted it there. Those bits would have migrated to the other MAGI as they linked with it for the attack on Tokyo 3. The commands she just issued would bring those bits together in the other MAGI's core systems and would take effect as soon as Maya let loose the other surprises which would flood them with diagnostic requests, error messages, repeated queries by the millions from the government systems they were linked to, and the vast contents of entire digital libraries from all over the world.

"They've hit the firewall," Maya reported. "It's holding. Everything looks good."

"Then let them have it Maya," she commanded with a smirk.

"Yes Ma'am!" Maya responded with unexpected glee. There was even a malicious little smile on her face.

Now it was a matter of waiting to see if the measures they had worked so hard on had any effect. The hope was that not only would their measures stop the attack but weaken it. They wanted the attacking systems to have to pull back resources to deal with the imminent threat to their core systems. Everything they had thrown at them so far was designed to push them to that course of action.

She spared a moment to look up to the observation level where Yui still stood with the Sub Commander. While the woman definitely looked concerned and worried, she wasn't in a panic. Yui caught her eye and offered a brief, small smile. She took that as a sign that the Children were okay. She knew that Lilith would be keeping Yui updated as she kept track of Shinji and Rei through her link to them.

 _'Bet Misato's wishing she was there with gun in hand to take on Kiel's goons.'_ Ritsuko smirked to herself. _'Knowing that they were targeting the pilots must have her in a rage. I don't even want to think what she might do in Unit 01 if anything happens to Shinji.'_

"Sempai, the strength of the hack is beginning to weaken," Maya said, breaking her out of her thoughts.

Ritsuko checked her screens and sure enough the incoming data flow that was hitting their firewall was slowly beginning to lessen. After a few minutes it began to drop much quicker. The enemy systems were having to takes resources away from the hack to try and protect themselves.

"Time to let them have phase two," she said.

Upon entering a new series of commands she unleashed a second wave of attacks. Whereby the first wave concentrated on overwhelming the enemy systems while the virus attacked their core programming, the second wave of attacks she unleashed would hit all of the secondary programming within the systems. While a lot of the peripheral programming and systems were less vital than that at the core, they were still pretty important in their own right and was data that they could not afford to lose. This two pronged attack meant that the enemy would have to decide which battle to fight since they couldn't fight both and they certainly couldn't maintain the hack while they fought either of them.

"Now that's a rather predatory smile if I ever saw one," Yui's voice from beside her.

"It worked," she grinned. "We hit them hard and their attack is now rapidly declining. They have too many problems of their own to worry about now to be attacking us."

"That's good," Yui sighed in relief. "At least when the Evangelions deploy they won't be operating blind."

"Speaking of which, are the kids alright?" Ritsuko asked.

Yui nodded. "According to Lilith their escorts are taking out anything that gets in their way. So far they haven't run into anything they can't handle. They had to tell Asuka a little bit of the truth, just enough to make her understand why other human beings were attacking the base. She's not holding them up but it hit her pretty hard."

"Not surprised," Ritsuko said. "Considering her views about NERV's importance and her status within it. Finding out it was all a sham would be crushing. Especially with all that she is already dealing with."

"Rei is determined and helping her along," Yui added. "And Shinji's nervous and he's scared but he's hanging in there."

"Sub Commander!" Hyuga suddenly shouted from his station. "We've just gotten word from the Pacific Fleet that they have radar contact with seven large aircraft that are on a direct heading for Japan. They're still outside our detection range however."

"Let me know the second you pick them up," Fuyutsuki ordered. He picked up the phone to let the Colonel know, although the man had probably received the same report already.

"Are the Eva's prepped and ready?" Ritsuko asked.

"They're ready to go and all systems are green," Maya answered. "We have no reports of any enemy incursions in the cage areas and all surveillance cameras show the cages are clear. They'll be able to launch on their own with no assistance from us if necessary." Hopefully that wouldn't be the case since it meant that in some way, shape, or form the bridge crew would be cut off or incapacitated. It was a necessary precaution however under the circumstances.

"I just hope it remains clear and they get there soon," Yui said. She wanted them _all_ there safely, but selfishly she wanted Shinji there most of all and she made no apologies for that. He would be all but untouchable inside of Unit 01 and under Lilith's care. Physically at least, but there was no armour or entity present with the Eva that could protect him from the stress and fear of the fight and her little boy had been through so much already. This should be the last battle he would have to endure, she prayed to any deity that was listening that it be so and that he could then have the peaceful, quiet life he deserved and with all of the love and care that he had never been allowed to have.

* * *

From the very beginning Kiel had always planned on being at ground zero when Instrumentality took place. It wasn't a necessity, he could be anywhere on the planet and be within the effect of the event, but he wanted to be as close as possible for the culmination of all of the hard work he had put in over the centuries to get to that point. Originally it was to be himself and the Committee in a conference room he had secreted in a surface building on the edge of Tokyo 3, but with the demise of the Committee he had revised that to a bolder and more preferred option that he had held in reserve.

Either way, he would be there for that moment. The point of renewal and rebirth, the much desired return to what he truly was. The point where he could resume the work of perfecting the ideal life form that was the balance between strength, power, and intelligence, a perfect balance that would allow it to survive and flourish against the challenges made against it by both its own brethren and other naturally occurring and evolving species. Beings that he could guide to prominence.

He had certainly known what a transgression he was making when he sent the second Seed to this world but he had sought to send a message to his own kind. The life forms produced by the two differing types of Seeds were inferior as far as he was concerned. The flaws within both of them made them vulnerable and with his brothers and sisters being so reluctant to guide these life forms as they grew and evolved it only made the situation worse. Without a guiding hand both types fell towards their ruination, finding a multitude of ways to squabble and make war among themselves and prey upon one another in ways both petty and depraved.

If the goal was to promote life then how could they allow this? How could they even start from the flawed stock they used and then simply content themselves to let it evolve as it may? To him that had been just as cruel and depraved as the behaviour of the unguided life forms themselves. How were they to ever know any different if there was no one there to help them along and allow them to prosper without destroying themselves. Just because their own race had begun this way eons ago did not mean that they should make every life form they were responsible for suffer the same way when they had the knowledge of experience to help them do otherwise.

There were others who believed as he did and the subject was a long and often debated one, but he had been the only one willing to do something drastic to make his point and illustrate as vividly as possible how flawed the current way was and to push his ideas for creating a better Seed. But he was seen as a villain. Others were doing experiments to the same end, but only he was willing to push the envelope and push theories that the others deemed as too dangerous and unstable. His experiments didn't take place in theory on paper or in a dish under a microscope, he created fully formed beings constructed of various ratios of the genetics of the Adam and Lilith type Seeds.

The failures were many. The test subjects either lost the structural integrity of their bodies through their AT Fields and fell apart, or grew into grotesque shapes and proportions and either imploded or exploded. Some of the few that lasted more than a few days displayed glimpses of unchecked power and psychological instability. Yet, every failure rendered valuable data to the process. In the end, once his research had been uncovered, he had been labelled a monster, a murderer who cared little for the pain his test subjects had to endure. A man who had become obsessed and lost sight of the true goal and the ideal of the sanctity of life. They said he was jealous and spiteful of the others who sought better ways in their own research that was slowly making positive headway.

They sought to reeducate and reform him by stripping him of his power and sentencing him to live among the inferior life forms on this world and spend all of his time and effort over several lifetimes to help guide and improve their lives as one of them. To do whatever he could to ensure that any life forms produced by the second Seed he sent did not awaken and affect life on this world. Today that long and excruciating sentence would come to an end and with it the flawed existence of the beings of this world. Their last contribution would be to rejuvenate him and allow him to continue on with his work. His revenge against his own kind would be the success of that work. He would prove them wrong. He would create as many test subjects as it would take to perfect what he knew to be possible and once he had he would seed worlds with them and guide them and show the others among the First that he had been right. His theories and his work would be justified and he would be vindicated.

Not even the alterations to his plans that had been necessary over the last several weeks would stand in the way of him being at ground zero. He would have preferred things to go according to his original plans but he supposed he was quite fortunate in how few snags there had actually been up until now. He would have preferred that his ability to turn both the Japanese government and its military against the Tokyo 3 base had remained intact. The object had been to neutralize the base and its personnel, primary among them being the pilots. No pilots meant no Evangelions to oppose him. Once the MPE's arrived the ritual would begin and there would be no risk to losing any of the units before hand.

Ikari's actions upon the return of his wife had thrown the proverbial spanner in the works but it was not a critical breakdown. Even with only seven MPE's at his disposal they should be more than a match for the remaining operational units should the mercenaries fail to neutralize the pilots and they would have no back up from the base with their MAGI hacked and taken out of the equation. Instrumentality would happen and he would have the souls of the remaining population at his disposal to set himself free.

Having overseen the construction of the Tokyo 3 base, even if from afar, he was aware of every hidden entrance and secret passage within it. He had ordered the majority of them to be constructed after all. He even knew of the handful that Ikari had seen to installing for himself and he would be making use of a couple of them. Thus far the trip through the dark and cramped secret spaces had been slow and tiring even though he was seated in his wheelchair. But they, himself, Dr. Holzer, his two best bodyguards Josef and Kurt, and two other men hand picked by them, had remained undetected thus far. By the time they reached a secluded portion of the parking garage that was restricted to Ikari's use only, the shooting had already started.

One of his few remaining moles in the place made sure that the power was restored to Gendo's private elevator from the car park after the SIS people had had it cut off. It would take them straight to the command level and hopefully with little trouble he would have his front row centre seat to his own last death and rebirth on this much loathed little world.

* * *

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	30. Chapter 30

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

 **Transposed**

 _ **Chapter 30**_

He was twenty feet from the last intersecting hall before they reached their left turn into the long hallway that led to the ICU. He had just made sure that his charges had gotten down low when two mercs wheeled around the corner, very nearly catching him off guard. His well honed reflexes served him well as he met their pistol fire with shotgun blasts while making sure he stayed between the mercs and the girls.

Two rounds smacked the wall head high to his left and two more whizzed very close by on his right as he stroked the trigger. The blast of buckshot almost missed the merc on his right entirely but just enough of it caught him in the hip to spin him around and send him stumbling away. His second shot left the barrel just as a nine millimetre round slammed into his vest high on his right chest and just below his collarbone, and a second whizzed too close for comfort by his right ear. The impact hurt like hell and knocked the wind out of him and his arm and hand was going numb. While he still had some feeling in it he quickly fired twice more. His last shot had missed but these two both hammered onto the man's body armour. It may not have penetrated but the force of the impact smashed his ribs and sent him hard to the floor. A bullet from the first guy skimmed across his left bicep and he sent his last two shots back high. One caught the guy in the chest, the second blew his head apart.

He dropped the shotgun and leaned against the wall, fumbling for the pistol under his left arm with his now mostly numb right hand while he tried to catch his breath. He managed to draw the pistol without dropping it and transferred it to his left hand. Advancing cautiously towards the corner he kept his eyes on the wounded merc as he writhed on the floor and struggled to breath. No one else came around the corner so he risked a quick look and saw that there was no one else. Turning back he saw the merc trying to reach his dropped pistol in the midst of his struggling so he put an end to him with a bullet between the eyes.

Walking back to the girls he began opening and closing his right hand and loosely shaking out his arm, trying to coax the feeling back into it. "Damn it that hurts," he groused. "Like getting kicked by a horse. Better than the alternative though."

Asuka was wide eyed. His vest may have stopped the round but this man had just taken a bullet on their behalf, had stood with bullets snapping by him left and right yet he seemed unfazed by it. She on the other hand was more frazzled than she had already been. Having been told that other humans wanted her and her fellow pilots dead had been hard enough to believe, but he had purposely stood between them and the enemy like a shield so that if anyone got shot it would be him and not them. She had feared the worst when she heard him grunt and saw him stumble when he was hit. She didn't know what her old self would have thought or how she would have reacted...no, she was all too aware of what she may have said or done, or at least the false bravado she would spouted.

Going to one knee, he picked up the shotgun and began reloading it. He could see the turmoil on her face and her eyes were glued to the deformed 9mm slug that was still caught in the outer fabric of his vest. He might not know exactly what was going on in the girl's head but he knew spooked, haunted, and confused when he saw it. She had become broken and now what she had thought of as a solid truth since she became a pilot and something stable she could cling to had been revealed as myth. In a nutshell people she had fought to protect were now trying to kill her and she had just seen an up close example of it.

"You hanging in there Asuka?" he asked her.

She was distracted enough that she startled a bit when he spoke. "I..." She closed her eyes for a moment and took a deep breath. That departed aspect of her would be screaming obscenities at her right now, calling her a coward and a wimp.

"You're scared and confused and at loose ends about what's going on and why," he surmised. She nodded as if ashamed. "Nothing wrong with being scared and you have every right to feel like your world has been turned upside down, because it has. I feel the same way."

Her eyes widened in disbelief. But he had stood there with no cover and fired back, like it was the most natural thing in the world to him. His only reaction had been to comment rather nonchalantly that it hurt. He didn't even seem to care that he had been shot. The bullet was still there damn it, lodged just millimetres away from his flesh.

"Even with as much combat as I have seen there is always still a bit of fear inside me," he continued. "It's natural and it actually can help keep you alive. And finding out about all of this that's going on, it turned my world upside down too. And inside out. It probably scared me more than the bullets do. Despite that fear I'm still here doing what I do and you are no different. Despite your fear you are still here too. You could be hiding under a bed somewhere or huddled in a corner but you aren't. You came with us to go to your Evangelion even though you don't know if you can still pilot it. That takes strength and guts."

"There is more to you than the part that is no longer there," Rei spoke up, astonishing her redheaded counterpart with her words. "You are still here and it is not."

"Well spoken Ayanami," Matt said with a light smile. "You're doing good Asuka, far better than many would under the circumstances and I can tell that you have the strength to keep going." He reached up and plucked the deformed slug from his vest and held it up. "I'm not sure if luck is something outside of our influence or if we make our own. Either way we can all use a little luck to go with our strength and it doesn't hurt to have something to focus it on to remind us." He gently grasped her hand an placed the slug in it. "Any bullet that doesn't hit you is a lucky one for you. I wasn't so lucky but all I got was a bruise so I'd say it's still pretty lucky anyway." He shrugged and smiled. "I know it's corny and I sound like a complete dork but what are you gonna do?"

She actually smiled a little as she closed her fingers around the slug. "I'll be okay, I'll make it."

"I know you will," he said, returning the smile as he stood. "Now, lets go."

They skirted around the dead and hurried up the hall, as fast as Asuka could manage in her walking boot at least. Honestly he didn't know how the girl _was_ still standing after everything that had happened to her both in her past and recently. He didn't know how any of the three pilots were still standing actually. He hadn't been lying to the redhead when he told her that she had the strength to keep going. Even if she was doubting herself and questioning her very identity he could see that she did truly have the strength within her to keep moving ahead. He hoped that he had helped a little with his words and his corny gesture, sometimes little things like that could mean a great deal and make a difference and he had been entirely sincere and hadn't lied to the girl.

She actually reminded him of someone he had known when he was that age. They had been close and in the desperate years in the aftermath of Second Impact she had fallen into despair and ended up taking her own life. He always felt like he hadn't done enough to help her, hadn't said the right things that maybe would have made a difference. Felt that perhaps he hadn't been there enough or done enough even in his own grief of having lost his entire family too. They had been friends since they were little kids and quite possibly would have become more than that. Maybe if he had had some wise words for her too he may not have lost her.

He hadn't showed it much outwardly when they learned the truth about Second Impact and everything else through the information Kaji had brought them, but he had been furious. Mel had been too. It had been tough enough when Second Impact was thought to be due to a meteor strike, but to find out that what had cost both of them so much had been anything but and been done deliberately...he didn't know how either of them had kept it together as well as they did. Mel had been far more demonstrative than he had been, but his relative silence had not been seen as a sign of indifference. It had been seen as the silent, murderous rage that those who had worked with him for years knew that it was. And he had taken it out on the enemy every chance he got.

He and Mel kept each other balanced just as they had since they first started working together. They gave the enemy no quarter but never lost sight of what their objectives were. Personal vendettas would only get in the way but that didn't mean that he hadn't enjoyed ripping gaping holes in SEELE's ranks or that he hadn't taken a certain amount of satisfaction from giving Gendo Ikari the forty five calibre lobotomy that he so richly deserved. He hoped that he would get the chance to wrap his hands around Lorenz Kiel's throat and squeeze the life out of the old alien bastard, but he had other priorities to take care of first before he went looking for the genocidal fool.

Reaching the end of the hall and their next turn, he took a look around the corner. He couldn't be sure but he thought he may have seen movement in the area of the nurse's station. It was far enough away that it was hard to tell and whatever he saw didn't repeat.

"We might have company up ahead so move as quickly as you can and stay alert," he instructed them. Getting a nod from both of them, he led them around the corner.

They made good time down the corridor, pausing only at adjoining halls before crossing them. The closer they got to the junction at the nurse's station, the more his instincts screamed at him and he had learned long ago to never ignore those instincts. He didn't know how many there were, but there were definitely some unfriendly types up ahead. It didn't take them long to finally show themselves.

Two men came charging out of a room on the far side of the nurse's station, across from the elevators. The same room Ayanami had been recovering in from her beating actually. The moment he saw them emerging from the room he banged off two shots. The first guy ducked but the second went down with a squawk like he caught a few pellets.

"Get behind the desk and stay down!" he commanded his charges.

He came around the bowed out front of the desk with the shotgun roaring. The first guy had risen to one knee and started firing his assault rifle. Rounds chewed up the top of the counter at the desk, a pair of them burning along the left side of his vest. His first round of buckshot hit the floor to the shooter's left, his second slammed into his assault rifle, jerking it from his grasp and mangling his left hand that had been bracing the fore stock. With him down and out for the moment, he whirled on the other guy who was shakily bringing his rifle to bear and trying to aim through the stream of blood rolling down his face and into his eyes. Shotgun pellets had slashed open his scalp and he was bleeding profusely.

A blast to the head took him out and he turned and let the other guy have the same. An inhuman growl and the sound of boots slapping the floor gave him scant warning before someone slammed into him and propelled him into the wall next to the nurse's station, his left shoulder taking the brunt of the impact. He swung back to his right, using his shotgun as an improvised club as he held it by it's pistol grip but his assailant had anticipated it and slapped it aside, knocking it out of his hands and into the nurse's station. The empty weapon clattered to the floor right in front of Rei and Asuka who were hiding under the desk.

As he barely deflected a follow up right cross from his attacker, he realized he needed to get the fight away from the two girls and he needed to get a little space to work with. Being backed against the wall and the side of the nurse's station, along with being turned a bit to his right was leaving him in a bad position to defend let alone strike back effectively. Taking the only move he had at the moment, he lashed out with his left foot, aiming for the guy's knee. He missed, but the hardened toe of his combat boot slammed solidly into the merc's shin bone a couple of inches below the targeted joint. It was enough to make him hiss in pain and take a step back.

As he pushed off the wall towards his foe, Riker saw what he was up against. They were pretty much the same size but this guy was obviously older with grey hair peppering his buzz cut. He had a nasty looking old burn scar up the right side of his neck to his jaw and numerous scars marked his face and bare arms. He wore standard OD green pants and a sleeveless black t-shirt, but no body armour. A pistol was strapped to his right thigh and that was the only weapon he could see at the moment. With the angry, somewhat deranged look in his eyes and the feral, snarling expression on his face, he seemed more beast than man. He looked like a man carrying a furious grudge but whether that was directed at him or just everyone the guy fought he didn't know, nor did he care.

He pushed off the wall and into his opponent while he was back on his heels, propelling him across the hallway and into the opposing wall. It quickly became a grappling contest and a test of strength. Neither could gain an advantage and began take shots with feet and knees to try and tip the scales one way or the other. They slid and rolled along the wall until the got to the doorway of Rei's former room. Slipping in the gore from the dead merc in front of it they tumbled and fell into the room. As luck would have it Matt ended up on the bottom.

He lost his grip on the guy momentarily and took a left in the face. He retaliated with a right and kept his arm up, pushing against the merc's chest to keep him back. The guy tried to knee him in the groin but he got his leg up and deflected it. The guy teetered off to his left and with his weight shifted he was able to slide out from under him. The old merc moved faster than he thought and lunged at him, catching him around the waist with a roaring growl, slamming him into a cart full of monitoring equipment along the wall next to the bed. He immediately began sledgehammering his fists down into the guy's back and it took a couple of hard shots to the kidneys to make him sag and loosen his grip, howling in pain. A knee lift shoved the guy back in a stumble and he came after him, crashing a right into his face that split his cheek open and sent him stumbling further back into the opposing wall.

To his credit the merc rebounded and came back at him and they went at it in a close quarters flurry of fists, knees, and feet. The guy was skilled and his obvious long experience as suggested by his age showed. It was a bit surprising though that his strikes were as under control as they were with rage filled look that seemed etched into his face, and the snarling and grunting growls escaping his mouth. It never failed. Every time he got into a fight like this it always seemed like he drew the oddballs and the crazies. It had been a while though since he had been this evenly matched. No matter, this fight was starting to go on longer than he was comfortable with. Rei and Asuka were out of his sight and he didn't know if there were any other hostiles in the vicinity.

They were matching each other blow for blow and block for block. His shins and forearms were getting sore from the abuse, and he knew he was going to have a pretty good bruise on the left side of his face. His bottom lip was split and blood was dribbling down from the corner of his right eyebrow, but luckily not into his eye. His opponent was looking a little rougher but still no less determined. Split lips, a couple of cuts to his face, a missing tooth and a broken nose, none of it seemed to bother him.

He heard a single gunshot from somewhere out in the hall and it broke his concentration, earning him a hard left that sent him stumbling back. He thought he had heard someone screaming out in pain but he couldn't really tell with the thunder reverberating through his head from the punch. He could feel the blood running from his nose and his cheek throbbed painfully but but thankfully it didn't feel like anything was broken.

"Hope the boss didn't shoot the blue one," his foe ground out in a voice that was low and so gravelly it was almost garbled. "That one's mine!"

Riker's vision suddenly turned red in rage. He disliked mercenaries on general principle, but bottom of the barrel scumbags like this one, deranged monsters who had long ago given in to the worst aspects of human behaviour, he hated with a passion. He had seen it all and every time he could do so he would gladly exterminate vermin like this from the face of the earth. Bad enough this...creature...had taken money to hunt down three fourteen year old kids, but he planned on turning one of them into his personal toy.

Fuck that and fuck this guy straight to hell.

As the merc moved towards him he grabbed the heart monitor from the cart he had crashed into earlier and swung it, smashing it across the guy's head in a shower of broken plastic and electronic parts. The merc howled loudly as it gouged a nasty gash in his scalp. The merc staggered and lurched toward him and he stepped into him, unleashing a right hand with all of his power behind it, feeling and hearing the cheek and orbital bone break and collapse under the impact. The merc slammed back against the wall and rebounded towards him and this time he was met with a left that hammered into his jaw, shattering it and sending a spray of blood, saliva, and teeth flying from his mouth. He hit the wall again and was met with Matt's right hand clamping over his face, a grip like iron squeezing. The old merc thrashed and clawed at him, his skull feeling like it was being crushed.

"Fucking pedophile," Matt growled. "If I had the time I'd squeeze until your eyeballs popped out and your empty fucking skull crumpled like a beer can."

He pulled the guy forward and rammed the back of his head into the wall, smashing in the back of his head with a sickening crunch. The old merc went limp, his eyes rolling back in his head. With a yank he tossed him aside and to the floor. He took a couple of seconds to suck in a calming breath before drawing his .45 and shooting the guy in the head. Twice, just to be absolutely sure before storming out of the room.

* * *

They had hit the floor inside the nurse's station immediately upon his order and had just slipped under the desk when bullets began chewing up the counter above them. Instinctively they tried to duck down even more and hoped that the bullets didn't start striking any lower. It was doubtful that the walls of the counter structure around the station were up to the task of stopping rifle bullets. Two single shotgun blasts told them the shootout was done, but then their protector was bulled into the wall off to their left and his shotgun clattered to the floor in front of them.

As Matt wrestled his opponent away from them Rei glanced at Asuka. Were her sense of empathy a little more developed she might have felt sorry for the redhead. She was shaking and looked little like the Second Child she was used to. While Asuka had not been terribly kind to her since they first met, or to Shinji for that matter, it gave Rei no great satisfaction to see her reduced to such a state. She noticed that she had her right hand tightly clenched around the spent slug Captain Riker had given her. While she had never given much thought to the value of such things, it seemed like that 'good luck charm' was doing exactly as he had hoped that it would. It was occupying at least enough of the damaged girl's attention to keep her from fixating entirely on the rotten situation they were in.

Rei had always known that an attack by humans upon the Tokyo 3 base had been all but assured so none of this was a surprise to her. Asuka however had dove headlong into the public purpose for which NERV existed, to safeguard the world against the Angels and to protect humanity. Unfortunately she had also mixed that with enough bloated pride and inflated egotism to choke a bull elephant. Gendo had counted on that and used it against her. He needed a true believer like Asuka. She could be easily manipulated to fight and follow his orders without ever realizing that her sole purpose was to be cannon fodder to keep Rei alive to fulfill her role, and further keep Unit 01 safeguarded until he could enact his version of Third Impact. To him she was largely expendable and it hadn't really mattered when or how she met her end.

They had told Asuka just enough to make her understand the gravity of the situation and if they survived this day she knew that she would want the rest of it explained to her. The question was just how much more damage would it do to her? She may be better off now with that arrogant and egotistical part of her seemingly dead and gone, but whether that would make the blow any less harsh was unknown.

The sound of boots clomping the floor in an unhurried pace gradually grew louder until a shadow loomed over them. Blocking the entryway they had used to get into the nurse's station was a tall, skinny, tanned mercenary with several days worth of scruff adorning his face and his seemingly short hair was covered by a forest camouflage do-rag. He wore black cargo pants and a black t-shirt, covered by an open green safari style vest adorned with pockets filled with his tools of the trade. A battered cigarette hung from the corner of his mouth. He held a worn looking MP-5 sub-machine gun canted over his right shoulder.

"Look what I found," he drawled as he fished a lighter out of his left breast pocket and lit his cigarette. "Fucking jackpot. Do you have any idea how much money I can sell the two of you for? Lots of dirty old men out there who'd like to pop the cherry of one of the famed Evangelion pilots."

"Y-you'd sell us for that?!" Asuka exclaimed, her voice a mixture of incredulity, fear, and a little bit of the old anger Rei was used to.

"Of course I would," he said, he tone suggesting he thought it was a stupid question. "Toss up though who would pay more, them or the Angel worshipping cults. Fuck, I could start a bidding war between them and more than triple the price. The cults will pay anything." He leered at them. "What they'd do to you would make the old perverts look tame by comparison. They'd beat you, pass you around for everyone to have a go at, then slowly torture you to death as a human sacrifice to appease their God because you killed his Messengers. I've seen their handiwork," he grinned sickly. "Nasty shit, they're a real bunch of wacko's."

"You took money to kill children and speak of selling them," Rei said coldly. Her tone shocked Asuka. She had never heard that much emotion in Rei's voice before. "What does that make you?"

If anything, his grin got bigger and sicker and his eyes roamed up and down Rei's plug suit clad body. "A smart businessman in the reality of the post Second Impact world. Besides, you want sick? You should see the amount of money old man Kiel dropped on us for this. Obscene fucking dollars and he doesn't even care what we do to you just so long as you don't make it to your Eva's."

"He'll stop you," Asuka blurted out. "He won't let you hurt us."

"Who, the big bastard that got you this far?" he laughed. "Fuck, Lindeman probably has him busted in half by now, that's why I hired the fucking lunatic. Needed an expendable piece of shit like him who wasn't afraid to take him on. Fucker and his partner got a reputation as people that you least want to fuck with or face down in a fight. The bogeyman that scares the bogeyman if you believe the hype. Lindeman's fucking nuts though, his brains are scrambled from being in the field too fucking long. All he does is drink and fuck little girls he pulls off the street, but with the proper motivation the dumb shit will do anything."

"You told him he could have one of us," Rei stated. It wasn't a hard equation to figure out.

"Smart girl Blue," he grinned again. "Not that I'll give him what he wants, he's just too much of a fucking liability to be associated with beyond today." He leaned in toward them, trying to intimidate them. "I think I'll keep the both of you, make a nice retirement gift for myself. Shit, you have no idea how bad that freak wants to stick it in your back door Blue, I'd be doing you a favour."

Rei felt a wave of disgust wash over her as she unflinchingly met his gaze. "I believe the appropriate response is 'fuck off'."

Impressed that she would stare him down and sass him like that he never saw her arm move, pulling the 9mm pistol from where she had kept it concealed behind her leg. But he did hear the bang and it took his brain a moment to register the searing pain and the sudden wet gush of blood as her shot obliterated his manhood. He screamed and hit the floor in agony, both hands clutching at his destroyed man parts.

"You fucking cunt!" he screamed as he rolled about in agony. Rei tuned out his cursing and screaming, content to let him suffer what he had earned and ready to give him another one if he he become a threat again.

The sound of two rapid pistol shots from down the hall startled her and put her on edge and it had startled Asuka as well. She had gasped and grabbed tightly onto her shoulders. The worst case scenario was playing through the redhead's battered mind. What if he had lost? That sick man would be coming for them now and not even the other merc would be able to stop him. She started shaking again as they heard the sound of boots quickly and heavily slapping the floor and getting closer.

"Ayanami! Soryu!" Matt called to them.

"We are here and unharmed," Rei answered. Asuka sagged against her in relief.

Matt quickly kicked the merc's MP-5 away and yanked a pistol from his right hip and a knife from his vest and tossed them aside. He took a look at the girls to make sure they were okay before turning his attention back to the groaning soldier of...misfortune.

"Nicely done Ayanami," he said, smirking. "You just neutered one of the biggest pieces of shit to ever walk the earth. Meet Conrad Dyson, scumbag of scumbags even in the world of guns for hire. Flesh peddler, rapist, pedophile...no low is too low for this asshole."

"Fuck you!" Dyson half yelled, half groaned. "I'll fucking kill all of you and I'm gonna skin that fucking cunt alive!"

Two rapid fire shots slammed into Dyson's chest, pulping his heart and silencing the merc. "That's enough out of your mouth," Riker said coldly as he stepped by the body and entered the nurse's station. He plopped down in one of the chairs and retrieved his shotgun from the floor and began reloading it. "Are you two really alright?" he asked.

"He did not touch us," Rei answered. "But his words and his intent was...disturbing."

"He was disgusting," Asuka shuddered. "A pig."

"Luckily no one has to worry about him anymore," Riker said. "You did good Ayanami, you protected the both of you. And your shot placement was rather fitting."

"Are you alright?" Asuka asked him quietly, noticing the blood from the cut on his eyebrow and the busted lip. The bullet crease on his left bicep was also oozing blood again.

"A couple of cuts and bruises," he grinned. "I get that much from sparring with my partner." He didn't let on that his face felt like he had been hit with a brick or that his arms and legs felt like he'd been blocking swings from a baseball bat. Overall he was largely unscathed and the discomfort was easily tolerable. He'd had a lot worse so this was nothing. Still, she seemed to be relieved.

"Did either of you hear anything that suggests we have more company nearby?" he asked as he set the shotgun aside and pulled his .45, removing the partially spent clip.

"Only him," Rei answered, looking in the direction of the dead mercenary.

"Good," he nodded as he slid the new clip home and returned the pistol to its holster. He clicked on his radio. "Zero-Three, are there any signs of enemy activity at the Eva cages?"

"Negative Zero-Three," came the answer from one of the comm techs. "It seems to be clear. Unfortunately there are no available friendlies in the immediate area either, they are all tied up in skirmishes."

"Copy," he responded. "We will be at the cages in a few minutes." He looked to his charges. "Ready?" They nodded. He grabbed the shotgun and stood. "Okay, lets go."

He quickly led them the short distance down the hall to the elevator and had them stop short and stay back against the wall. He stood between them and the elevator and pressed the call button, keeping his shotgun at the ready. The doors opened almost immediately and he tensed waiting for any sounds movement from within or the sudden eruption of gunfire. After a silent three count he whirled around the opening, shotgun leading the way and ready to blast anything inside that didn't belong. Thankfully the car was clear. He held the door open with his foot and waved them in, keeping an eye out for any late arrivals from down the hall. Once they were in he joined them and let the door close.

"Stay as far to the front as you can and up against the wall," he told them. He had taken up position in the front corner of the car opposite them. "If anybody's waiting for us and opens fire we'll be out of their immediate line of sight." _'Hopefully,'_ he thought.

He pushed the button for their destination and took the time to observe the two pilots as they were lowered deeper into the base. Rei looked a bit troubled, a slight frown marring her face. He knew that the last time she had ridden this particular elevator it had been when she desperately tried to reach her Evangelion so that she could launch and help Shinji as he was attacked by the Fifteenth Angel. That attempt had ultimately ended in failure and he had been told that even though she displayed little outwardly about that it still bothered her a great deal. Part of her struggle with her newfound emotional state. Someone she cared a great deal for had been in pain and needed help and she had been unable to reach him. That would be hard enough for most people to deal with but when the particular feelings that went with it were something that she was largely experiencing for the first time, it hit her all that much harder.

Asuka, she looked even more nervous than she had all the rest of the time since the attack started. He'd been filled in on that possibility too. The prospect of getting back into the Evangelion, something she hadn't done since she discovered that the soul of her mother resided within it. That revelation alone had turned everything she thought she knew about her Unit 02 right on its head. It wasn't just a mere tool or weapon for her to wield and it didn't operate solely on her much self promoted skills.

She had no idea if she could sync with it anymore. She already apparently felt enough guilt about what she had done and that her actions had left Shinji all alone to carry the fight, but if she could contribute nothing now when her skills were truly needed the most it could very well destroy her entirely. There was also the possibility of communication with her mother's soul now that she knew it was there and the fear that she couldn't, or even worse, that she would be rejected.

When the elevator reached their destination and the doors opened he listened intently for any sounds of activity. The ambient noise from machinery and electrical equipment wasn't all that loud but it was just enough that he wasn't going to hear much beyond a few feet away if someone was trying to be quiet. Taking a deep breath and letting it out slowly he headed out the door, his shotgun up and tracking as he quickly but thoroughly scanned their surroundings. When he was satisfied that the area was indeed clear he called for the girls to join him.

Unit 00 was almost directly across from them and Unit 02 was in the next cage bay down to their right. Unit 01 stood at the far end to their right and he could swear that it was watching him as he kept constant vigil over the girls as they made their way to Unit 02. The steep walkway up to the plug was a challenge for Asuka and her booted right foot, but Rei simply slung the girl's arm over her shoulder and her own around her waist and got her to the top without much trouble. Whereas the old Asuka would have been offended by the help and who it came from, this Asuka quietly thanked the blue haired girl with a rather down look on her face, no doubt due to the reasons why she even needed any help.

"I have forgiven you already so there is no need to worry about it," Rei offered simply. If only it could be that simple for Asuka. Forgiving herself was going to take time, but in response she simply nodded and tried to smile.

While Rei was getting the plug open Asuka kicked off the hospital slipper on her left foot and began undoing the walking boot on her right. She was having a little trouble because her hands were shaking.

"I'll do it," Matt told her, laying down the shotgun and going to one knee in front of her. He unfastened the clasps and straps and opened up the air cell padded shell so she could pull her foot out freely. Her foot was still well wrapped in bandages and she could put some weight on it but kept most of it on her left foot.

"Thank you," she said.

"You can do this Soryu," he said confidently, causing her to meet his gaze. "You're a strong girl and whatever else you may have lost, you didn't lose that strength. Being here now and going through what we did to get here proves that and I think you have a different kind of motivation now than you did before from what I have been told. I believe that you can do this."

She looked up at her Eva. "It's not the same now, it's all different."

"Change can be unsettling, but it can also be good," he said. "It might even be better. Remember what you want to do and why you want to do it, then make it happen. You're the only one that can."

"Right," she responded, a small bit of confidence seeming to return to her.

"It's ready," Rei announced. She handed Asuka her A-10 clips.

Asuka simply looked at them for a moment and when she finally put them on it wasn't in her usual fashion as if they were glorified hairpins and worn to show her status to all who could see, she simply affixed them in place and limped to the opening of the entry plug. Before Rei assisted her in entering the plug Asuka turned and gave him the closest thing to a smile that he had seen out of her. He nodded and returned the gesture. He didn't know if he had been any help to her with anything he said but he hoped he had helped to bolster her confidence even if only just a little.

After closing the hatch Rei rejoined him and they made their way over to Unit 00. At the bottom of the ramp she returned his pistol to him, making sure the safety was on and handing it over grips first.

"Thank you for escorting us Captain," she said.

"No problem Ayanami," he responded as he returned the pistol to the holster strapped to his right thigh. "Just wish it had been a little less eventful."

"Under Commander Ikari's plans this was inevitable," she said. There was a bit of...something in her voice that spoke of the distaste she felt for her role in his plans and how accepting of it she had been.

"He's dead, you're not," Matt said bluntly. "Time to write a different end to the story. Personally I like happy endings, like the girl robot pilot getting the shy boy robot pilot and living happily ever after."

Her face reddened. Kind of adorable really. "I would like that very much to be true," she admitted softly.

"Well, your future is yours to make now, so go give them hell and make it happen," he said. "I'll keep an eye on things down here and wait for Mel and Shinji."

She didn't know what else to say so she simply nodded and turned to go up the ramp. She stopped and turned back, unzipped her plug suit and retrieved the clip for his pistol that she had stuck between her breasts earlier and gave it back to him. Zipping back up she turned and hurried up the ramp.

He couldn't help chuckling as he slid the spare clip back into his vest. "Girl needs to work on her modesty." He waited until she was inside the entry plug before he began walking in the direction of Unit 01. He keyed his radio. "Zero-Three, Pilot's Soryu and Ayanami are safely inside their entry plugs. I'll be making sure things stay vermin free down here until Zero-Two and Pilot Ikari arrive."

"Roger Zero-Three," came the response.

"You owe me another fifty bucks Mel," he chuckled. "I got here first."

He walked part way up the ramp then climbed over the rail and onto the framework that locked down Unit 01 and held it in place. Finding a good spot about two thirds of the way up where he could see the majority of the cage area, he sat down and leaned back to wait. He could use a bit of a rest anyway right now. He glanced up at the face of the infamous 'berserker'. "Hope you ladies don't mind if I keep you company for a bit until Shinji arrives."

Unit 01's eyes glowed briefly, seemingly in agreement.

"Yeah, that's not freaky at all," he smirked and settled in to wait for his partner to arrive.

* * *

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	31. Chapter 31

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

 **Transposed**

 _ **Chapter 31**_

There was no physical reason for it to be so, but sitting in the entry plug felt very different, almost alien to Asuka. It felt like it was the first time she had ever been here. She had been here a thousand times or more, spent countless hours in sync tests, simulations, and actual combat, yet she felt almost like she had no idea what to do. All she could think of was what a phony she had been. She had seen herself as the best pilot, someone to be treated like a celebrity and given all the respect that she felt she deserved.

But she hadn't earned any. She had treated everyone around her like dirt, like they were so far beneath her that they were practically unseen. She had indeed trained hard, but how did that make her the best pilot? She jumped into her first battle as if she was going to make easy work of the Angel and she was going to show that lucky upstart Ikari how it was done. But she would not have won without his help and she was pissed because of it. She learned nothing when she leapt foolishly into her second battle and was made to look like an idiot. She hadn't won a single battle on her own as she kept so ignorantly boasting that she could if others would just stay out of her way and stop stealing her glory.

That seemed to be the only thing she had been interested in. Glory. She only ever paid lip service to the idea that every battle was a world saving endeavour. The most important thing to her was winning for her own sake and glorifying her achievements and it didn't matter if she had to ridicule, embarrass, and denigrate her fellow pilots to do it. Then to make matters even worse she loses her mind, nearly beats Rei to death, and leaves the fight for Shinji to fight alone.

Now here she was stripped of all of that pride and egotism, sitting here shaking and afraid, unsure if she could make Unit 02 work. Unsure if she would be of any use in this fight. Both unsure and afraid of trying to sync and making contact with her mother. She wanted to. Mama had meant everything to her and to see her after the Eva had split her soul had been devastating. Of course she didn't understand it at the time so she never realized that half of her mother's soul was still within the Eva and that it had been with her the entire time as she trained and fought...and as she protested that the machine was nothing but a tool, a weapon that worked only because of her prodigious skill.

"I'm sorry Mama," she said shakily. "I've been such an idiot."

She closed her eyes and took a deep breath. Sitting here feeling sorry for herself was not going to do anything to determine if she could still pilot and start making up for the things she had done by getting into the fight again. She began the start up sequence, allowing the plug to begin filling with LCL.

"Unit 00 beginning startup," she heard Rei call over the radio.

Automatically after years of practice she regulated her breathing in anticipation of filling her lungs with LCL. It felt weird to be feeling the fluid through her hospital pyjamas, the plug suit always acted like a diver's wet suit and she hadn't felt like this since that aborted naked sync test in the simulation bodies.

"All systems are go Rei," came radio traffic from the bridge. "You're sync rate is steady at eighty two percent. Unlocking restraints and moving Unit 00 to the catapult."

Asuka's eyes were bugging out as she watched the restraints retract from Rei's unit and it was pulled back and onto the catapult rails. Eighty two percent?! When did she hit that high of a rate? She was never close to that before! She'd be lucky if she could get high enough now to even make Unit 02 move at all.

"Don't fall apart now Asuka," she shakily whispered to herself. "They're going to need all the help they can get. They're counting on you and he said you could do it. You can't keep letting everyone down."

"Unit 02 initiating startup," she called over the comms. "Please Mama, I know I don't deserve it but I need your help. I know you're here now and I won't try to shut you out. I know it's not just me operating the Eva. It's us."

She opened up her mind as the plug lit up and began to cycle through start up. At first she didn't feel anything, fearing that it wasn't going to work so she sought it out more aggressively. She began to feel the rudiments of contact when everything suddenly shut down.

"No!" she cried, tears beginning to leak from her eyes.

"Try again Asuka," a soft, calm voice she had never heard before told her over the comms. "Just relax and don't push so hard this time. I think she's just as nervous and afraid as you are."

"W-who are you?" she asked.

"I'm Shinji's mother, Yui Ikari," the voice answered. "Just let the contact come naturally as it always has for you. It will work."

"O-okay," she answered. She settled herself down and tried again, letting herself fall into the long known routine. She felt the old familiar pull again, felt her mind coming into contact with the beast and she let it take its course this time. Her senses seemed to elongate and she could feel the larger body of the Eva as if it were her own, only it seemed...fuzzy, not as sharp and clear as she remembered it."

"Start up successful," Yui's voice told her. "How does it feel Asuka?"

"It's fuzzy," she answered. "It feels kind of heavy. My sync rate isn't very high is it?"

"You're currently holding at forty four percent," Yui told her. "Which considering everything you've been through is quite good actually."

She brightened up considerably. She was above the minimum to make the Eva move. "Then...I can fight? I can go help Rei and Shinji?"

"If that's what you want to do," Yui said. "No one is going to force you if you don't think you can."

"I want to help!" she blurted out quickly. "I've already done enough harm so I want to help in anyway that I can. If I can fight, then I'll fight."

There was a moment of silence before Yui responded. "All right then, get ready Asuka. Releasing restraints and moving Unit 02 to the catapult."

For the moment there was nothing else she could do until launch. "Are you there Mama? If you can't talk to me...or don't want to...it's okay. I just need to feel that you're there." When there was no response of any sort she hung her head and tears came to her eyes again. She wasn't going to give up though, she was still going to go out and fight, but she had hoped to make contact with her mother before she did.

She raised her head and gripped the controls. She would go out and fight beside her fellow pilots, her comrades who had been good enough to forgive her despite everything rotten thing she had done to them. When they defeated the enemy, when all of this was finally over she would start doing whatever she could to make up for her transgressions. She didn't want to be the old Asuka ever again and she was going to do her best make sure she never was. Captain Riker had told her, ' _Remember what you want to do and why you want to do it, then make it happen. You're the only one that can.'_ That was exactly what she wanted to do, both here and now today and in the future.

Just before launch she felt a sensation envelop her in mind and body. It was warm and comforting, a mother's loving embrace. Deep inside her mind she heard a whisper in a voice not heard for a very long time.

 _'I am with you my little Asuka. Always.'_

* * *

 _ **Elsewhere, with Mel and Shinji**_

They had made it to the stairs with no further incident, but that wasn't the case upon exiting into the halls outside the maintenance area. They had met resistance almost immediately and had gotten bogged down in a protracted firefight. They had taken concealment in a deep doorway while their adversary had entered a room down the hall and was firing from the doorway. Between them a merc lay dead on the floor and there had been a third guy but she didn't know where he was now. He might be lying wounded in the room or around the corner down the hall, or he could be looking for a way to flank them. Either way, she couldn't waste a lot of time here. The other pilots had already reached the cages and the MPE's could arrive at any time. She would rather the pilots had the advantage of all being able to lie in wait for them, if at all possible.

Firing another tri-burst down the hall she ducked back in anticipation for the return fire, which came as she was feeding a fresh magazine into her rifle. She was contemplating making a rush down the hall in an effort to end this when she heard a noise in the ceiling out in front of their position. A split second before she could raise her rifle two shots sounded out. There was a ventilation grill there and the large ceiling tile in front of it burst apart as rounds tore through it and slammed into her chest. She fell back into Shinji and with at least a little luck on her side her finger tensed on the trigger. Through her own motion of her rifle rising as she fell back, she sprayed the ceiling with a three round burst and was rewarded with a choked scream and someone falling through and into the hall.

She couldn't take immediate advantage however since she couldn't breath and it felt like a freight train had hit her head on. Her arms and shoulders were partially numb and she dropped her rifle. She nearly blacked out and was aware of Shinji frantically calling her name.

"Fuck it hurts!" she wheezed. "Son of a bitch shot me in the tits!"

She noticed the guy in the hall stirring and groaning in pain, a discarded .45 lying on the floor a few feet away from him. On instinct she rolled off of Shinji and into the hall, fumbling a bit as she pulled both of her pistols. Her plan, such as it was, was to shoot the guy in front of her and fire a few rounds down the hall to keep the other guy occupied. She succeeded in the first part, two rounds nailing the struggling merc in the lower spine and kidneys. As she fired down the hall with the pistol in her left hand a boot crashed into her already sore chest and pinned her to the floor. As she cried out in pain and tried to bring her pistols to bear she found a rifle muzzle suddenly and rudely shoved into her mouth.

"Stop moving or I blow his brains out!" the guy commanded. She froze and saw the merc had a pistol in his other hand and it was aimed right at Shinji. "Drop your pistols." Now that he was close she recognized who it was. He was one of the mercs who reportedly had left the estate with Kiel. Richard Schmidt.

She did as he commanded and tried to glare a hole through his head. She was also desperately trying to catch her breath without choking to death on the flash suppressor of his rifle. It was hot too but fortunately not enough to burn her, but it sure as hell wasn't pleasant. It didn't help either that he still had his boot pressing down on her chest, and oh fuck did it hurt.

Shinji was shaking like a leaf, scared for both of their lives. "D-don't hurt her," he stammered.

"Boy, why do you think I took Kiel's money in the first place?" Schmidt asked him coldly. "It wasn't so I could hunt down and kill children, though I have no reservations about putting a bullet in you if it keeps her in line or drives her to despair. Either outcome is acceptable. I took his money to hunt down this bitch and her partner for what they did to my men fifteen months ago."

"You're doing this for revenge?" Shinji asked.

"Her and her partner broke up an operation my men were involved in," he said. "That in itself doesn't bother me, it's the price one pays in this line of work. Not everything is going to go your way no matter how much you want it to. But they couldn't leave it at that. For the next thirteen hours they hunted my men down like animals through the ruins of Marseilles. In the end only five men out of twenty four made it back home. Men that I trained and served with in both the military and as a private contractor, and she cost me two more here today." He glanced at the downed men around him. "That cannot go unanswered."

He moved the barrel of his rifle deeper into her mouth, causing her to gag and choke. He let it go on for several seconds until the desperation of not being able to breathe filled her eyes. He kept his foot firmly pressed against her chest so she couldn't take much more than shallow breaths in her attempt to recover. He wanted to prolong that suffocating sensation.

"I will give her to my remaining men for a few days to do with as they please, just so long as they don't kill her," he explained. "Then she will die, slowly, painfully, and publicly as an example to all who would interfere in our business."

"How could you do something like that?!" Shinji blurted, clearly distressed at what he had just done and what he proposed to do.

"Very easily boy," he smirked. "I have little in the way of a conscience and I will do whatever it takes to get what I want be it power, influence, or money. Lives are cheap bargaining chips and I will trade or ruin as many as it takes to get what I want."

What he got at that moment was something he wasn't expecting. That's what happens when you pay more attention to the harmless, shaking, unarmed boy in front of you than the experienced combatant under your boot who you think is no longer a threat.

While Schmidt was momentarily distracted with his gloating, Mel grabbed the barrel of his rifle and pushed it up and out of her mouth and rolled to her left. Schmidt's finger tightened on the trigger, sending a three round burst into the base of the wall as he lost his balance and stumbled with her movement. She squirmed around and kicked out her left leg to tangle it with his and make sure he hit the floor. As he did she pulled on the rifle and wrenched it from his grasp. She tossed it aside and kept kicking at him, knocking the pistol from his left hand as he tried to awkwardly swing it toward her. She hammered the hardened toe of her right boot into his back a couple of times for good measure before rolling away and getting to her feet.

Now able to breath freely, she sucked in lungfuls of air as fast and as much as her aching chest would allow, and spitting out the acrid taste of metal and gun powder residue. A quick glance told her that Shinji had done the sensible thing and retreated back into the doorway and further away from Schmidt. The was no danger that the merc could grab him now without her getting in his way. As for Schmidt, he rose from the floor, stretching his back due to her kicks and was chuckling darkly.

"I should have known that you wouldn't give in so easily."

"Why the fuck would I?" she rasped. "I have a job to do and it isn't finished yet." She smirked at him. "His fellow pilots are waiting for him, they've already made it to their Eva's." _'And I owe Matt fifty bucks for that too,'_ she thought sourly. _'along with the fifty for the mercs that actually tried to parachute into the Geo-front. Why the hell do I keep betting him? I lose every damn time!'_

"So Dyson failed," he mused. "Typical of him to not hold up his end of a job. He puts his own sick, self interests ahead of everything else. Your partner's work I presume?"

She grinned. "He does love to crush sickos and put em' where they belong. Now, are you going to keep trying to talk me to death or are we going to get at it?" she drawled. Her grin became predatory and her eyes burned with rage. What he had done to her and what he said was going to happen to her was making her blood boil. "The souls of your dead men must be squealing like fucking pigs for their revenge and you have a few left that I haven't killed yet. I'll have time to hunt them down after I'm done with you."

She got the result she was looking for. Schmidt didn't rush at her in an uncontrolled rage, but he was clearly very angry and came at her with long, purposeful strides and definite ill intent. If he was hoping to intimidate her he was going to be sorely disappointed. She was a skilled hand to hand combatant but what most of her foes didn't know or take into account was the fact that she liked to fight. Actually, she _loved_ it. She discovered just how much she loved it back in high school and it hadn't mattered who she faced off against.

The snotty, debutante crowd who hated her because she wouldn't act like them or be their friend. It was all about who you knew and hung around with and her family had more money and connections than most. Members of the slap, scratch, and pull hair school of fighting got a rude awakening when they got a stiff left jab to the nose and a right cross to their pretty little mouths. Didn't help them much either when they tried to gang up on her.

The girls from the other end of the school's social and economic ladder who hated her for her looks and her family's money didn't fair much better. A few of them could fight but they still insisted on too much hair pulling and slapping. Guys started challenging her too and didn't fare any better. Some got whupped because they couldn't keep their hands to themselves and some challenged her just so they could grab a handful. The grabby types always ended up with broken bones. Thus, she avoided a great deal of the shit that came down when the football team's star quarterback suffered a broken nose, jaw, and dislocated elbow on his throwing arm the night before the state championship game. Every guy who hadn't been able to take no for an answer and who got grabby suffered the exact same injury. His guilt was therefore never in doubt.

The fights got better and more challenging after she joined the military. She wasn't allowed to bust up her comrades who got handsy, but she was allowed to make sure they got the point not to do it again. She ran into too many though that wouldn't take her seriously or tried to be chivalrous during training. She could take her lumps and expected them to fight her seriously. Beyond her instructors themselves, she wouldn't find someone who would seriously fight and train with her until she met Matt and getting hammered by one of his punches or kicks was all the incentive she needed to keep getting better so it didn't happen again.

She didn't like getting knocked out.

In the field, most of her opponents seemed to have an ingrained sense that they could easily outmatch her simply because she was a woman. Even at her size she often faced opponents who were bigger and stronger than her. The key was to not let their strength and power overcome you or wear you down and she had studied various fighting styles and borrowed from them all in order to accomplish that. Dodge and avoid, deflect blows rather than blocking them. She could brawl with the best of them and she enjoyed that the most, but by necessity she had learned how to flow around her opponent and not let them bog her down or wear her down with their physical advantages.

Schmidt was at least five inches taller than she was and easily weighed at least a hundred pounds more, probably closer a hundred and twenty. Despite his anger his punches and kicks were still largely in control and not wild or overdone. But she knew that the longer he went without being able to land a significant blow, the less patient and controlled he would become, he was not calm enough to do otherwise and it wasn't going to help that she kept that same predatory and somewhat amused grin on her face. It would continue to piss him off just like it had when she taunted him before the fists started flying. She doubted that he was underestimating her, he was too experienced for that but he was carrying a grudge and was angry. He wanted to make her hurt as much as possible. She could work with that.

She also needed to remember that she couldn't waste a lot of time right now. More mercs could arrive at any time and the safest place for Shinji was in his Eva, not to mention that the MPE's could show up at any moment and their best chances to survive was to have all three Evangelions on deck to greet them. Trying to hurry this up though carried it's own dangers but Schmidt wasn't the only one who had incentive and anger on her side. Her task wasn't finished yet and that mercenary bastard had stuck his gun in her mouth, had her gagging and choking for air when he tried to shove it down her throat. He planned to let his men beat and gang rape her until he decided to kill her in a public display. She was ready to explode on this mother fucker and she'd had enough of dodging and deflecting. She'd seen enough of how he fought.

He threw a left at her which instead of deflecting she hooked with her left arm, then pivoted and drove the heel of her right hand into his elbow. There was a sickening crunch as the joint dislocated and bent the wrong way. While roaring in pain he managed to stomp at her legs and caught her behind the right knee, causing her leg to buckle and she hit the floor but rolled away before he could follow up.

"Is that the best you got old man?" she taunted.

Big oops on her part because she assumed he would be at least momentarily preoccupied with the pain of his dislocated elbow. Instead he charged her. That's what she got for being cocky and letting her anger get the better of her. She knew better than to fuck around and this wasn't the first time her anger had gotten her in trouble. It was her biggest flaw. Usually it was a fight in a bar somewhere and not on a job and her partner was always standing at her back even if she didn't need him to.

She knew what it was. Even when she had been shot two years ago and was lying in a pool of her own blood she hadn't felt as helpless as she did when this fucker had his boot on her chest and his gun in her mouth and never mind the psychoanalytical, phallic power imagery of it. Helplessness was like a disease to her. She had felt helpless for years under the demands of her family until she finally found the strength and will to start rebelling against it and she worked hard to be and stay as strong and independent as possible even if she had to essentially isolate and insulate herself from others and go the lone wolf route to do it.

As strong as she was though she was still human and did struggle and have moments of doubt. Everyone did, even that big polar bear of a partner of hers who was never far away and who would poke and prod her back into shape or even just listen if she felt the need to talk. While his slips weren't as noticeable they were still there and she did the same for him. It was just one of the reasons why the bond between them was so strong.

The belief in and the strength she drew from that bond was something she was going to need right now to weather the onslaught as Schmidt slammed her into the wall. His right forearm was slammed into and pushing hard against her painfully throbbing chest and the back of her head walloped the wall hard enough to make her see stars. Sneering at her the whole while, he slammed his left forearm into the wall next to her head and with a jerk of his shoulder she heard the elbow joint pop back into place. And just to prove that he was none the worse for wear, he drove his left fist into her side below her ribs. She would have doubled over if his other arm didn't still have her pinned to the wall.

He switched arms, using his left to mash her into the wall and reared back with his right fist. She tried to fire off a punch aimed at the nerve cluster under his arm but missed and his fist crashed into her face, breaking and bloodying her nose. The fist crashed into her face again, splitting her left eyebrow open. At the same time she fired a knee into his short ribs. She tried for a second one and he sent a knee back at her, straight between her legs. With her left foot braced against the floor she managed to twist just enough that he caught the inside of her thigh rather than hitting dead centre. She nearly went down and would have if he still didn't have her pinned. Her head was spinning and it felt like there was blood trickling down the back of her neck. Those two punches had both pounded the back of her head into the wall again. She had to get out of this position.

He threw another right that she blocked and held off and fired another knee back at him. He deflected it then fired off three quick, hard punches into her gut. That last one drove the air out of her lungs and left her gasping for breath. She would have thrown up if there was anything in her stomach.

"You're not looking so good right now Captain," he taunted. "And you aren't talking shit anymore. You seem to be having a bit or trouble, yes?"

"I may have...gotten ...carried away," she said haltingly through gasping breaths. "Maybe we should...kiss and make up."

She slammed her forehead into his face as hard as she could, smashing his nose. His hold slackened on her and she kept going, giving him three more in rapid succession. He stumbled away from her, his nose crushed and his left cheekbone broken. She sunk to one knee, desperately trying to regain her breath through the pain in her chest and ribs and her broken nose. Her vision swam for a moment, the headbutts not helping the abuse her head had already taken.

Snarling in rage Schmidt came at her. Her intent was to let him get close enough that she could spring up from her current position and ram her shoulder into his guts. Unfortunately the knee she had taken to the thigh had given her something akin to a Charley Horse and instead of launching up and into him, she more or less wobbled toward him. He caught her around the throat with both hands and hauled her up, heaving her back towards the wall again with a roar. She couldn't get in that position again. As her back was hitting the wall again, this time with her feet off the ground, she speared the first two fingers of her left hand into his right eye, destroying the orb.

As he released her and screamed in pain, falling away with his hands clutched to his face, she rebounded from the wall and crashed to the floor, rolling away from him. Spotting his rifle next to her on her right, the thought of it having been shoved in her mouth made her anger rise again. That and anger at herself for getting handled like this because of it. Picking it up by the barrel she stood and stalked over to him. The angry adrenaline boost energized her a little and when she was within range she swung for the fences. It was a bit awkward since her left leg wasn't cooperating, but it was still a good swing.

The well used weapon's synthetic stock broke into pieces as it met his skull, sending him reeling and stumbling drunkenly back into the wall before crumpling to the floor. Eyes burning with rage and revenge and nearly hyperventilating now she stumbled up to him and rammed the barrel into his mouth, smashing several teeth in the process.

"How the fuck do you like it bitch!" She pulled the trigger and a three round burst mangled the connection between his spinal column and his brain and blew out the base of his skull. She just let go of the rifle and limped away across the hall. Leaning against the wall for support she concentrated on finally regaining her breath as she returned to the doorway.

"You still with me there Shinji?"

The boy peeked around the wall and judging by the look on his face she must have looked bad with the blood on her face. "Mel-san!" he exclaimed and came to help her over to the doorway. She couldn't help but smile a little as she felt the adrenaline rush leaving her. Even though she had told him to just call her Mel, he still added the honorific.

She sat down next to the door, reaching over and pulling her rifle closer. "Can you bring my pistols over here Shinji?" She knew he wasn't terribly comfortable handling guns but he had done alright in training. She knew he never wanted to have to use one against anybody and she hoped he never had to. Although he had seemed to enjoy just plunking targets on the range. He did as she asked and she noted that he made sure the safety was on before he picked them up and brought them to her.

She returned them to their holsters, then undid her vest, slowly and painful taking it off. It was tight enough and just heavy enough that it was making her chest hurt way too much to keep wearing it. Her breasts felt like over tenderized meat and there was the possibility that something in her upper rib cage or sternum could be cracked or broken. She'd have to take her chances without the vest's protection from this point. The discomfort with it now was just too distracting.

Shinji knelt in front of her. "Are you okay?" he asked meekly.

"Been better," she admitted, her voice a little raspy. "Got too angry over what he did and didn't keep a level head. Paid a price for it. You'd think I'd know better."

"What he said..." Shinji began, clearly looking uncomfortable at bringing it up.

"It was true," she answered. His shoulder's slumped. "But he wasn't telling the whole story."

"What do you mean?" he asked.

"As people scrambled to survive after Second Impact, all sorts of wars and conflicts broke out for just about every reason imaginable. Sometimes it was over food, shelter and resources, sometimes it was rival politicians and warlords trying to takeover or control territory. Sometimes it was just to try and settle old hatreds in the chaos. It didn't take long for the market for hired guns to explode and everyone who ever had a notion of becoming a soldier of fortune soon took up arms.

A lot of those groups became nothing more than paid terrorists or hit squads for their employers, some just became roving bands of thugs. It became such a serious problem that there was a summit conference being held in Paris attended by the defence ministers and top military brass of several countries to iron out a new strategy to deal with them."

Shinji's eyes widened. "His group was going to attack it?"

She nodded. "Didn't actually know for sure that they were his people until he confirmed it. He kept himself pretty well shielded. We don't know who paid them but it had to be someone with deep pockets because that crew didn't come cheaply. A concerted crackdown by the UN and the most powerful countries was going to be bad for business and someone decided to do something about it. If they shot up the conference and killed a bunch of high level people like those attending it could very well have killed the entire initiative and caused even more chaos.

Matt and I happened to be closest to the area when the information about the planned attack became known and the Colonel sent us in with orders to not just disable their ability to launch the raid, but to do everything we could to wipe them out entirely. It was to send the same kind of message to the mercs and their backers that they were trying to send to the rest of the world. They were camped out and training in the area around the destroyed port of Marseilles. We didn't get them all, but we got most of them and destroyed all of their vehicles and equipment and stopped any ability they had to get to Paris and launch their attack. It made the attendees at the conference take the situation even more seriously than they already had been and their countries have been hitting the mercs, their backers, and their financial set up hard ever since."

"Would he have really done that to you?" Shinji asked. "What he said..."

"Yeah, he would have," she answered as she wiped some of the blood away under her tender nose. "And he wouldn't have thought twice about it or lost any sleep over it. Truthfully I'd rather he shot me when he had the gun in my mouth than go through that, but since he's dead that's not a worry anymore. By the way, I should thank you. You held his attention long enough for me to get out of that mess."

"Oh, um, I really didn't do anything." He lowered his head. "I was so scared I could barely move."

She struggled to her feet. She was sore and was stiffening up and felt pretty tired at the moment from the adrenaline crash. "Don't sell yourself short Shinji. For some reason even the smartest of bad guys always seem to feel the need to gloat and you were his audience. That divided his attention just long enough for me to act without getting my head blown off." She placed her hand on his shoulder and he raised his head. "Besides, you weren't the only one that was scared. I damn near shit myself." She ruffled his hair. "Now, lets go find that partner of mine and get you where you need to be."

 _'And hope Matt doesn't go all mother hen when he see's the mess I am.'_

Fifteen minutes later, much of it spent with her left arm over Shinji's shoulders for support, they reached the cage area without running into any more opposition. It was kind of amusing. Her leg was all but useless at the moment and Shinji had been eager to help her if he could. The boy's face had been bright red the whole time though, close proximity to the opposite sex, especially if he found them attractive, was something he still had difficulty with. It had been the same during training when he was with Rei and when she walked them through the explanations of what certain moves did and how they worked with up close, slow speed, physical demonstrations. Though she wasn't terribly attractive right now. She was bloodied and bruised and smelled of sweat, blood, and gunpowder.

She adjusted the earpiece for her radio, which was now hanging on her belt since she ditched the vest.

"Zero-Two to Zero-Three," she called. "Is the welcome mat out for us?"

"Zero-Three," he answered. "The door is open and the path is clear. I'm standing by here keeping Unit 01 company."

"We're coming in."

She looked to Shinji. "Ready?"

He nodded. "Ready."

Hitting the button to open the door she let her carbine lead the way as they cautiously entered. If Matt said it was clear then it was. Even so, not being cautious was asking for trouble. There were a lot of little nooks and crannies people could hide in or pop out from all over the place. At the other end of the room they could see Matt climbing down from the gantry structure that helped secure Unit-01 in place. He waited for them on the wide walkway in front of the purple Eva, shotgun ready and his eyes roaming all over the cage room.

Even with the questioning, raised eyebrow he was giving her over the condition she was in, she had a feeling of relief and familiar comfort go through her at the sight of her partner. She did note the blood on his face and arm and the hole in his vest.

"Rough date?" he asked with a crooked grin. "Really Shinji, you have to be more careful with her, she's delicate."

She had to try not to laugh at the gasping fish look on Shinji's face. It would hurt like a bitch if she did. She knew she'd have to explain what happened but she was glad that he chose to engage in their usual banter right now instead. "I'll show you delicate," she shot back with a grin of her own, giving him the finger as she pulled her arm from around Shinji's shoulders. "Besides, it looks like the girls were a little rough on you too big boy."

He shrugged. "That's what happens when I hang around pretty girls. But they only have eyes for Shinji here it seems."

"Speaking of which," she said, looking to Shinji who had turned a whole other shade of red. "You'd better go. They're waiting and probably as worried about you as you are about them. You've got your own battle to fight and we aren't finished with ours down here."

"R-right," he responded. He started up the ramp to his Eva, but stopped and turned back toward her. He bowed. "Thank you Mel-san."

She smirked and winked. "Give em hell Shinji." He gave her a shy smile and jogged up the ramp and climbed into his entry plug.

"Nice kid," she said. "Polite too. _He_ treats me with respect. You should try it some time."

"Not gonna happen," he smirked. "Besides, you'd think I was sick or something if I did."

"Probably," she grinned. She went to her radio. "Zero-Two, the Third Child is safely inside Unit 01." There was no response. "Zero-One did you copy?" Still nothing. A look passed between them as he reached for his radio. Maybe hers just wasn't working now?

"Zero-One to Zero-Two and Zero-Three," came the Colonel's voice before he could try his radio. "We copy and we have a situation. Kiel, Dr. Holzer and four other men have gained entry to the command bridge and sealed all of the entrances in or out. Hostile units in the vicinity are keeping us from getting to them."

"Zero-Two, we're on our way," she called.

"Fuck!" he swore. "Takes some balls to show up there like that. Cocksucker thinks he's untouchable this close to the end."

"And with him there he'll keep the bridge crew from doing anything," she said. "Those kids will be fighting without any help from them."

"Let's go." He turned and started for the door at this end of the cage area. He was several feet ahead of her due to her gimpy leg when she heard a burst of rifle fire. She felt rounds go past her head and her heart nearly stopped when she saw one slam into the right side of her partner's back, below his shoulder blade. With a grunt he pitched forward and hit the metal floor.

Rage filled her mind as she pivoted towards the sound. She made too good of a target out here in the open but it didn't matter much since there was no cover in the middle of the walkway anyway. Lady luck was smiling on her however. She found her target standing in the walkway about sixty feet away near an opening that led to a ladder for one of the maintenance cranes. It looked like he was desperately trying to clear a jammed casing from the ejector port of his rifle. She pumped out two three round bursts and took him down hard. A quick survey of the area told her that there was no one else visible. At least for the moment.

"Matt!" she called as she backtracked to her partner. A pang of relief shot through her as she saw him getting to his hands and knees.

"Fucking shit that hurts," he groaned.

"Did it go through?" she asked as she looked at the hole in his vest.

"Yeah," he grunted. "But it didn't go far."

Keeping a close eye out for more hostiles she helped him out of his vest. "Can you keep watch while I check it out?" she asked.

"Yeah," he answered as he took her rifle and turned so he could see the majority of the room. If any one else showed up he would need something with more range than his shotgun.

She tore open the hole in his t-shirt a little wider so she could get a better look. The slug had penetrated all the way through his vest and its deformed remains had penetrated his back. Maybe a sixteenth of an inch of it still protruded outside his flesh.

"I can pull it out," she said. "Just deep enough it's gonna hurt like a bitch though."

"Already hurts," he said. "Go for it."

He tensed as she dug her fingers in around the slug to get enough of a purchase on it. With a sudden tug she pulled it free and tossed it aside.

"Thanks doc," he grunted as he handed her back her rifle and picked up his shotgun. "At least you won't have to carry me."

"That's twice they got you today," she groused. "I saw the hole in the front of your vest earlier."

"What about you?" he asked. "You aren't wearing your vest."

She sighed. "Got me twice too." She pouted and winced at the same time. "He shot me in the tits Matty." It came out almost like a whine.

He grinned cheekily. "Want me to check out _your_ wound too?"

She swatted him. "Fuck off," she croaked. "Don't make me laugh. It fucking _hurts_ every time I breath. Shit, it hurts every time I move _._ "

He started for the door again. "Well, try not to bounce too much, don't want you to make it worse."

She growled at him, but was grinning slightly. "Why do I put with you?"

"Nobody else can stand you and somebody's gotta watch your back," he countered.

"You sure that's not just so you can look at my ass?"

"Eh, gotta take the benefits where you find them. Now let's go see what we can do about getting through to the command bridge."

* * *

It was a good thing for Shinji that he had been busy with the start up of Unit 01 and wondering why he wasn't getting a response from the command bridge. He didn't see what had happened. He liked those two. They had done a lot to help him and Rei get ready for today and had risked their lives to get them here. However once his vision came up through the Eva's eyes he did see them exit the cage area. And five seconds after they did that end of the room exploded in a shower of dust, smoke and debris.

* * *

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	32. Chapter 32

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

 **Transposed**

 _ **Chapter 32**_

"They are coming," Rei intoned calmly as she watched the sky above Tokyo 3. High up, just on the edge of her unaided vision she could see the seven figures of the Mass Production units as they jettisoned from their transport aircraft.

They were set up on the edge of the old district of Tokyo 3, the area where she used to live. Hopefully they could keep much of the battle contained to this part of the city. With all of the habitable buildings in the city's core now underground there was just open ground here and a collection of derelict buildings. Fortunately this was something that was planned ahead of time since they had lost contact with the Command Centre shortly after they launched. It also meant that they could not gain access to any weapons storage buildings or spare power umbilical cords since they needed Command to raise them. They would have to face their foes in hand to hand combat and with no other weapons than their progressive knives.

She had filled Asuka in on what she knew about the MPE's and in particular the nature of their weapons. If the interrogated scientists that the SIS had rounded up were correct, they would be facing weapons that could slice through their AT fields and do damage directly to them as pilots as they did to the Evangelion's themselves. Not just sympathetic pain through synchronization, but real bodily damage as well.

As if that wasn't enough, while it hadn't actually been fully verified the scientists had intimated that even after suffering critical damage the units would still be capable of moving so long as the core or dummy plug was intact and functional and there was power to run the unit. The dummy plug was essentially a single function control unit. It's only purpose was combat and once activated it would continue to execute its function until destroyed or the until the unit itself was rendered physically incapable of movement. With the MPE's having artificial S2 engines they essentially had an unlimited power source. Whether or not they could regenerate damage like an Angel could due to the power of that S2 engine was unknown, but thought to be unlikely.

There was also the possibility that the Seventeenth Angel was among them in whatever form it took. If it happened to be within one of the MPE's, Rei surmised that it should be easy to find. It would have an AT field whereas the intelligence that had been gathered from the captured scientists suggested that the MPE's did not. The reports on the two captured units showed that they were also more lightly armoured than Units 00, 01, and 02. They would be relying on the faux Lance's they carried and the programming of their dummy plug's to make up for it.

"We can do this right?" Asuka asked.

"We can," Rei answered. "There is no other choice but to do so and succeed. If we fail the world ends."

"I hope Shinji gets here soon," the redhead said. "It will be easier with all three of us." Truth be told, she was actually worried about him. She wouldn't openly admit to such a thing but it was for different reasons now than before.

"He reached the cages shortly after we launched." As soon as the words left her mouth Rei knew she had said too much. But she was worried about him too and had said it mostly as a reassurance to herself that he was indeed safe.

"How do you know that?" Asuka asked.

"That is another explanation that will have to wait," Rei told her. "We have more pressing matters at the moment."

Rapidly circling down towards them on wings of their own, it didn't take long for the seven mass production units to land before them. They were mostly white with black accents and from the neck down they were very close in design to their own units, really only missing the shoulder pylons. The heads however were nightmarish. There was no differentiating between head and neck, they were eyeless and sprouted from between the shoulders like some sort of long, fat, white worm. The mouths were large and lined with sharp teeth with large red lips. A blood red tongue hung from the mouth as if it was too long to remain inside. Large white wings with black undersides folded up behind them as they landed. Each one held a double bladed weapon nearly as tall as it was with a handle in the middle of it.

"Ugh, creepy," Asuka scoffed. The damned things were even drooling which fit into the image perfectly.

"One is staying further back than the others," Rei observed.

"Do you think it's the Angel?" Asuka asked.

"Unknown but it would seem to be a reasonable assumption," she answered.

"I just wish my sync rate was higher," Asuka sighed. "It would be helpful."

"It may be lower but you still know how to fight," Rei said. "Do not think about it. Let your training and your instincts lead you. I will take the right side, you take the left."

 _'What happened while I was in the rubber room?'_ Asuka asked herself. _'Rei seems to be more outgoing. She's not such a doll anymore. She's taking charge instead of blindly following.'_

"Right," she responded. Follow her training and instincts. How could she ever forget that, it had been drilled into her head repeatedly for years when she was training in Germany.

She and the units closest to her moved at about the same time. One thing she noticed right away was that they weren't as quick on their feet and their posture when they moved seemed to be hunched over. The one closest to her took a forehand swipe at her with its blade. She pivoted around it and launched a back heel kick into its spine, sending it crashing into the unit next to it. The third one jumped over its comrades and swung its blade down at her. She side stepped the left handed strike and launched an uppercut. Unit 02's armoured right hand slammed into the underside of the MPE's jaw, collapsing it as if it were made of paper mache. The teeth shattered and broke as they slammed together, severing the lolling tongue. The entire mouth end of the worm-like head exploded in a shower of broken teeth, bone, and pulverized, bloody flesh.

The one that had been knocked down by the first unit rose up to meet her and she swung a sweeping kick at it, obliterating the entire head to within a couple of feet of its shoulders. It joined the second unit on the ground, blood gushing from the stump of its neck. She gave herself some room from the first one as it slowly rose back to its feet, cracking sounds coming from its back as it straightened up.

The intel Rei had given her was correct, these units were not nearly as heavily armoured as theirs were which she found to be a very strange thing. If the lack of tougher armour was meant to make them lighter and faster that advantage seemed to be lost in their somewhat sluggish physical movements. Was that a product of the way the dummy plug synchronized with the systems since that meant there wasn't a living, breathing pilot with their hands on the controls? When its dummy plug had been activated Unit 01 hadn't looked that sluggish on the footage she watched after the battle with the Thirteenth Angel.

As she readied herself to meet the the first MPE's next attack, she suddenly realized something. Her connection to Unit 02 didn't feel quite so fuzzy now, like her rate of synchronization had increased. It was feeling a little more like it used to and her movements thus far had come to her naturally. Unconsciously when the fight had started she had stopped thinking about her lower sync rate and if she would be of any use in this fight. Once the action started she did indeed fall right back into the movements of her training, moving instinctively as she had learned to do over so many years of hard work.

As good as she was feeling right now she wasn't about to fall into the cockiness of that departed side of herself. If what Rei said about their weapons was true then it would only take one decent blow to land to give her serious trouble. She would also have to keep an eye out for the two she had already damaged. If they really did have that S2 engine and could do what was suggested, she would really need to try and aim to destroy the cores and plugs. It would be easier if she had a weapon to use. She may have to try taking one of theirs if they still couldn't expect any help from the bridge. Until an opportunity to do so presented itself or she was able to land blows to the core and plug, she would just have to keep doing as much damage as she could, however she could.

Rei buried Unit 00's right fist into the guts of the first MPE to attack her, shattering the light weight armour and driving shards of it into the flesh beneath. The MPE vomited a large quantity of blood and she flung it back into the unit behind it. Its core was partially exposed now but she couldn't strike at it as the third unit lunged at her. She sidestepped the swing of its blade and swept its legs out from under it. Grasping the right leg by the ankle she savagely twisted it counter clockwise and pulled, not just tearing the leg armour and the knee joint apart, but literally tearing the leg right off at the knee.

The first unit was coming back at her again and she used the severed limb as an improvised club, smashing it over what passed for the back of the unit's head, pulping the flesh and sending the unit face first into the ground. The unit it had crashed into earlier stepped up and she backhanded it with the severed leg, smashing through it's teeth and ripping open the left side of it's mouth. With it's mouth hanging open in such a grotesque fashion, she shoved the leg down into its throat and kicked it away from her.

The one with the severed leg swung its blade at her from its grounded position. She hopped over it but unfortunately it caught her umbilical line, severing it. The warning alarm sounded and the timer countdown began as she landed. Her left foot crushed the hand holding the lance and she kicked out with her right, pulping most of the thing's head and neck in a spray of blood and gore. Reaching down she picked up the MPE's weapon and sliced it from crotch to throat, opening up its guts and cutting through the core and the entry plug. The enemy unit went still. For good measure she stepped on the remains of the plug to ensure that nothing was left alive inside of it. It was a savage action but that was what was required to win this fight.

She had hoped to last longer than this before her umbilical was cut. She would have to eject before the timer ran out, being stuck in the Eva without power was a death sentence if any of the MPE's were still operational. It was a near certainty that the cable would be cut at some point but she had wanted to be further along than this. Soryu seemed to be holding her own and hers was still intact for the moment. What they really needed was the advantage of Unit 01 and its inexhaustible S2 engine. She supposed the reason for his delay was because of the loss of contact with the command bridge. He would have no assistance from them in launching and would most likely have to push his way out of the cage and climb up to the surface if this turned out to be anything more than just a communication problem.

She couldn't risk the loss of concentration on the task at hand to try contacting Lilith. She would just have to hope that Shinji would arrive here soon. They might be able to severely disable or outright destroy the six MPE's they were fighting, but if the seventh one which still hadn't joined in was indeed the Seventeenth Angel, they wouldn't have a chance without him.

* * *

 _ **Earlier**_

Just as Unit 02 was making its way to the surface the door to the command bridge opened and three large men dressed in black and carrying HK MP7A1 PDW's stormed into the room and promptly shot the four NERV security personnel stationed in the area. Two on the main deck and two in the lower deck area.

"Move back away from your consoles...do it now!" one of the men barked at the startled bridge crew. With three gun muzzles aimed their way they all complied and rolled their chairs back away from their stations. One man had his weapon pointed up at the Commander's station and ordered Fuyutsuki and Kaji to stand in view with both hands visible on top of the railing.

"Clear!" one of the other men called back towards the door once they had moved. Immediately another armed man entered along with a thin, bald, middle aged, ghoulish looking man and an old man in a wheelchair with a mechanical visor over his eyes.

"Chairman Kiel," Yui said as she rose from her seat. She stepped between Kiel's entourage and the bridge crew, looking rather calm with her hands shoved into the pockets of her lab coat. The body guards all turned their weapons toward her but Kiel held up a hand to back them off.

"It's alright, " he told them. "But if anyone else moves do not hesitate." He turned his attention back to Yui. "Dr. Ikari," he acknowledged. "I had never expected to see you again after your contact experiment. I would be very interested in knowing how you came back. You should have accepted my invitation."

"If you had actually asked me yourself I may have," she responded coldly. "I did not appreciate your men accosting my son and I on the street. Fortunately some concerned bystanders came to our aid."

"Yes, the rather bothersome SIS," he all but growled. He glanced up at the main screen which showed Unit 00 and Unit 02 deploying into the old part of the city. "It seems that they keep interfering and the Second Child is not as incapacitated as I was led to believe."

Dr. Holzer moved to look at the console in front of Maya. "Her sync rate is forty four percent and stable," he reported to his boss. "More than enough to be able to pilot effectively...and the First Child is at eighty two...far higher than what where were last apprised of."

"A lot of things seem to have gone against you lately Chairman," Yui said. "And they will continue to do so. My son will be in Unit 01 shortly. Your mercenary army has failed to stop the pilots from getting to their Evas and your hack on the MAGI has failed."

It was harder to tell with his eyes hidden by the mechanical visor he wore, but the tightening of his jaw and the scowl made it obvious that Kiel was not happy at either piece of news.

Holzer nodded. "If it had worked they should not even be able to view the outside and all consoles are still streaming data." He looked coldly at Dr. Akagi. "How did you manage to hold off a hack by all of the other MAGI?"

"We didn't just hold it off," she smirked, making him scowl. "We stopped it dead and turned the tables on them. We are free and clear while they are all under attack themselves."

"Inconveniences," Kiel growled out, cutting off any outburst the incensed Holzer was about to make. "But nothing that will derail the end result. Such failures were considered and it matters not if there is a slight delay because of it. And with all of you held at bay Unit 01 will not pose a threat. The unit cannot launch itself and will remain locked in its cage. Even if it were to launch the other two will be reduced to scraps by the time it arrives."

"I wouldn't be so sure of that," Yui cautioned him as she turned to the main view screen where Asuka and Rei were beginning to make a mess of the MPE's. There were gasps among the bridge crew when Rei ripped the leg of off one and used it as a club before ramming it down another unit's throat, then opened another from crotch to head with one of the MPE's own lances after it had cut her umbilical.

"We know their weakness and how to kill them so you have lost that element of surprise," she said. "I assume however that you decided to put the Seventeenth in that seventh unit? I see little reason otherwise for it to be sitting back and waiting. We do know you have control of the last Angel Kiel, what Gendo didn't know outright about your plans, he deduced with a great deal of accuracy it seems."

"Yes, I may have actually underestimated his ability to pry into things that should have been no concern of his," Kiel said. "You are correct on both counts and that is exactly why things will end as planned despite however many roadblocks you think you can put in the way. What happened Dr. Ikari? You used to be just as committed to Instrumentality as any of us were."

"I had ten years to think about it and realize what a blind and naively idealistic fool I was," she answered. Her gaze on him turned hard and cold. "And I also discovered what an enormous lie Instrumentality was. It had nothing at all to do with mankind's evolution being stalled or with ending all human suffering and replacing it with a godlike, mindless nothingness." Her icy stare pinned him to his wheelchair. "I know what you are Chairman and I know exactly what your Instrumentality is intended to do."

* * *

 _ **The Cages**_

Shinji was wide eyed in horror at what he had just seen. He sat frozen as the smoke and dust swirled around before him and debris pelted the catwalk and gantry work in front of him. They had just went through the door and now the entire end of the room was a pile of rubble. They were just right there!

 _'Shinji,'_ Misato called to him softly over their link through Lilith.

"M-Misato...they...they were just..."

 _'I know,'_ she said.

"W-we have to help them..."

 _'There's nothing we can do for them right now Shinji,'_ she told him. _'If they're still alive and you tried digging in there with the Eva you could make things worse.'_

"Bu-but..." He could feel Misato's presence wrap around him and hold him.

' _Rei and Asuka are fighting the MPE's and need your help Shinji,"_ she reminded him gently. _'And your new friends fought to make sure the three of you made it here to have that fight and so you could fight together. I know it sucks to not stay and help them but even they would tell you that you have a job to do and that you need to go and do it. You just have to trust that they are still alive.'_

 _'We will have to break our way out,'_ Lilith said. ' _Kiel has taken over the bridge so they won't be launching us or be able to offer assistance.'_

"Mom!"Shinji cried out, panic seizing him.

" _She is alright,"_ she assured him as she too wrapped him up in her presence. _'She and the others are just being kept from their tasks and are unharmed. If need be she can defend herself, I've made sure of that so you don't need to worry Shinji. She will be fine."_

"A-are you sure? I can't lose Mom again."

 _'You won't lose her Shinji,'_ Lilith said softly. _'You have my word that no harm will come to her and she will be waiting for you when this is all over.'_

 _'We made the same promise to her about you Shinji,'_ Misato told him. _'She's just as worried about you and we'll do what ever it takes to protect you. We love you Shinji and we won't let anything happen to you or her.'_

He closed his eyes tightly for a moment at took a deep breath to settle himself. As sad as it sounded he still hadn't quite gotten used to there being people who cared so much about him. Misato, Lilith, Rei. Even his mother. He had gone so long without knowing her love that it was still strange and new and almost bewildering to him just like it was with the others. Even Asuka's whole attitude toward him seemed to have changed to a much more positive and accepting one. The love and positive feelings from all of them was what had been keeping him upright and still going after his ordeal with the Fifteenth Angel. It was what had been keeping him moving forward knowing that this day was coming.

"Okay, so how do we get out of here?" he asked shakily.

 _'Leave that to me_ , _'_ Lilith told him.

They could literally tear their way out but there were numerous lock bolts in the gantry work and restraint mechanisms that were seated directly into Unit 01's armour. While those locking bolts, or more likely what they were attached to were likely to give way before the armour did, there was still the possibility of doing damage to the Eva itself. Unit 01 was essentially her own body now with the near infinite power of its own S2. By manipulating her AT field she covered the Eva with it like a second skin then flared it, slicing through all of the locking bolts and clamps that held her in place. If Kiel saw what Unit 01 just did from his seat in the command bridge he would shit himself.

 _'Alright Shinji, now we can push the gantry bridge out of the way then we'll go to one of the recovery elevators and go up that way,'_ Lilith explained.

"Won't we still need help from the bridge to use the elevator?" he asked.

 _'We don't need the elevator, just the shaft,'_ she said. _'It's bigger than the catapult shaft. We'll fly up through it the same way we flew up to kill the Fifteenth.'_

That flight was a blank to him, he'd either been totally out of it or unconscious at the time so he'd missed it. At least it would be faster than climbing up to the surface in the same way he, Asuka, and Rei had to when they fought the Eighth Angel. Moving the gantry away from from the Eva was pretty simple, even with there still being hydraulic pressure in the system's hoses. Unlike the launch against the Eighth, the lines had not been cut to release the pressure holding the gantry in place, but Unit 01's strength was more than sufficient to overcome it. The lines would probably burst from the back pressure but that was of little consequence right now.

The harder part would be getting to the elevator. The back wall of the entire cage area was a series of doors. When launching the doors behind the units would open and the Eva would be moved back to the catapult launch rails on its carriage. Between Unit 01's current cage and the ones that had been occupied by Unit 00 and Unit 02, there was another door that led to the elevator system. Mostly it was used when the Evangelions were recovered after a battle. They would be moved from the elevator platform to a carriage which would then carry them to the cages and set it in its designated place.

They moved from the cage to the blank section of wall and using the AT field like a wedge they pried the doors open enough to get the hands inside and use Unit 01's raw strength to spread the doors open far enough to pass through and into the carriageway beyond. Fortunately all of the various blast doors between here and the surface had been left open as part of the contingency plan should the Eva's have to launch under a no power condition, if the catapults were no longer working, or if the bridge could not aid in the launch. The door at the surface was still closed of course but they could get out easily. So long as the MAGI was still functioning any elevator door at the surface would open if an Eva approached it. The key was the Eva's automatic telemetry signal.

With the orange haze of its AT field enveloping it, Unit 01 began to rise up through the elevator shaft, picking up speed as it went. As it neared the surface the massive elevator doors slid apart and it took to the sky, spreading its AT field into wings and soaring over the scene of battle.

The MPE she had kicked in the back lunged at Asuka and she brought up her knee into its guts, stopping it cold and doubling it over. Easily picking it up over head, she brought it down back first across her knee, shattering the armour and breaking its spine. She pushed it aside and ducked as the unit with the smashed up mouth charged at her, its lance scoring a shallow cut down her upper left arm as it flashed by, spreading its wings and taking to the air. She bit back the scream of pain that came to her lips and grasped at the wound. Blood began to cloud the LCL around her arm as it bled. She had really been hoping Rei had been wrong about those lances being able to do direct damage to them through their sync but now she had proof otherwise.

She had little time to think about it as the other headless unit came at her. She fell to her back and kicked at it, nailing it in the side and knocking it away from her. Unfortunately the strike from its lance cut into her umbilical. It didn't sever it entirely but it was still useless now. Getting up she ejected the umbilical plug and picked up the lance that had belonged to the unit with the broken back and met the strike of the flying unit as it swooped back. Sliding off the clash of blades as it passed by she took a wild swing at it and gashed one of its feet. A bit of luck was on her side as she momentarily lost balance and a strike from the unit that had already wounded her made a shallow cut down her back rather than biting deeply. It still hurt like a bitch though.

She spun at it and it deflected her blade and thus began a dance of glinting steel as they swung and swiped at one another. She had to also try and keep an eye out for the flying unit as it circled around them looking for an opening. At one point she lost sight of it for a moment, catching it out of the corner of her vision almost too late when her grounded opponent had forced her to step back away from it. She ducked down and it missed her but the unit she had been sparring with lunged at her. Running on instinct she opened the right shoulder pod and fired off the large, black spikes contained within. Several of them pierced the MPE's torso, their tips sticking out of its back. Two went through the core, one through the entry plug. The rest destroyed internal organs and its spine.

The unit fell on top of her and she wasted little time shoving it off and picking her lance back up to face the flying unit as it swept back and landed, its own lance at the ready. Off to her right the damn unit with the broken spine actually began to crawl toward her, dragging its useless legs behind it. She would have to stay out of its reach while she battled the other one. Time was getting tight as she only had a little over two minutes left now.

Rei found it slightly disconcerting to be trading blows from her borrowed lance with two MPE's whose heads were little more than pulped and bleeding stumps of meat that just flopped about aimlessly as they fought. It didn't seem to hamper their fighting abilities in the least though since she was hard pressed to fend them off. A cut to her right leg and across her abdomen attested to that and while not terribly serious they did sting and burn.

The MPE's didn't seem to be able to work well in tandem however. She supposed it could be due to the fact that whoever it was that was used for the downloads for the dummy plugs had little or no experience in working together with a partner in battle. While the MPE's dual attack was relentless and tireless, it was not coordinated. They simply struck one after the other with no concept of one unit keeping her occupied while the other struck at the same moment or from a more advantageous angle. It kept her hard pressed and made attacking them back rather difficult.

The fight was falling into a pattern and she needed to change the rhythm and break things up or else they would eventually tire and overwhelm her. She jumped back away from them and to one side, the angle placing one unit directly in front of the other. When the front one charged at her she spun out of its way with a long step and swung her lance, catching the second unit which was following close behind and trying to come around it. She got it in the back and cut it in half just above the hips, blood and guts cascading from the horrid wound. She didn't get much of a breather as the remaining unit came back at her. Their blades clashed over and over, sparks flying with every strike.

As her timer hit the one minute mark she knew she would have to eject soon. She wasn't looking forward to it since there was really nowhere to hide where the MPE's wouldn't find them and there was nowhere nearby where they could get back into the Geo-front. If Shinji was here there was always a chance that they would be able to get inside Unit 01 with him, it was the safest place they could be.

She took another cut to her left arm but it allowed her to cut off her opponents left leg at mid thigh and causing it to fall down. She jumped back and put a considerable amount of distance between them in anticipation of ejecting. A few seconds later Asuka did the same, her last opponent at least momentarily incapacitated. At that moment a large elevator door in the ground opened up off to their right and Unit 01 shot into the sky on wings of orange light. It veered toward them and landed a short distance in front of them, a protective barrier between them, four mangled but functional MPE's, and the one pristine unit that had yet to join the battle.

* * *

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	33. Chapter 33

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

 **Transposed**

 _ **Chapter 33**_

"Do you now?" Kiel said coldly. There was no way possible that she or anyone else could know what he was or the true goal of his plans for Instrumentality. Least of all someone who had been trapped and isolated within the core of an Evangelion for the last ten years.

"You were exiled here as punishment," she continued. "For sending Adam here and going against the fundamental beliefs of your own kind when it comes to interfering with the development of life on the worlds you've seeded. Does that convince you that I know what you are Chairman?"

For the first time in a very, very long time, Kiel was surprised and caught off guard. How? How could she possibly know? The only possible source would have to be someone from his own race and they would never reveal who and what he was to anyone who was not one of them. Yet, he could think of no other way that she could possibly know. The only other explanation was that she was one of his kind masquerading as Yui Ikari and that was just as ludicrous a notion as the first.

"What kind of nonsense are you spouting woman!" Holzer exclaimed accusingly. "You make no sense. Did you leave part of your mind inside the Eva like that failure Soryu?"

"As unpleasant as ever," Ritsuko scoffed. "And just as crass. Plagiarize any other scientists work lately Herr Doktor? Wouldn't be you if you haven't."

"Still a catty bitch I see," Holzer sneered. "And still riding on your mother's achievements."

"Enough," Kiel grunted. Though he was glad for the two scientist's sniping at each other, it had given him a moment to collect himself. "What would lead you to such and strange and outlandish accusation Dr. Ikari? You must admit that it sounds like something out a fantasy story, not something I would expect from someone of your reputation."

"I suppose it does," she conceded with an amused look. "But the same could be said of SEELE and the way it has its tentacles in nearly every government organization across the globe and how it seeks and often succeeds in controlling events to their liking. We both know that to be true and it has been for a long time."

"Even if it does that certainly makes more sense than the nonsense you were spouting," Holzer interrupted again.

She turned a vicious glare on Holzer. She had always found him to be an arrogant, research stealing pig and just wholly unpleasant and she'd had enough of him. Despite her misgivings about the personality changes she had noticed in herself due to her time exposed to Unit 01's brutal nature, she was rather pleased to see that her sudden ire, the menacing aura she was able to project, and the glare she pinned him with was scaring the hell out him.

"Shut up," she seethed. "Do not speak again." After a moment she turned her eyes back to Kiel. "I have a very reliable source for my information Chairman. An Angel told me. The Second Angel, to be precise."

Holzer either followed her warning and stayed quiet, or else he was too flabbergasted to speak. Kiel did speak, though his hands were clenching the arms of his wheelchair in a white knuckled grip. "Such a thing is not possible Dr. Ikari. Do not try my patience any further with this ridiculousness."

"You wanted to know how I knew the truth about you and I told you," she countered. "You also want to know how I was able to return from Unit 01's core and I know you want to know how Unit 01 was able to manifest its AT field into wings in order to fly up and kill the Fifteenth." She pinned him with the same stare she gave Holzer. "Here's your answer Chairman in the form of a question. What is it that you think lives inside the shell of Shogoki's armour?"

"That is impossible!" Holzer exclaimed, having turned white as a sheet.

"It's not only possible, it's a fact," she said, pinning him with another glare. "You already know that the Evangelions develop their own rudimentary consciousness, that's why a human buffer is required in order for a pilot to be able to make them work. Obviously it needs to be someone who has a vested interest in the pilot, someone who will protect them from that raw and bestial consciousness and what better candidate than the pilots own mother. Or in the case of someone like Major Katsuragi, someone who cares deeply enough about them to be able to adequately fill that role. But it is much easier to accomplish if that consciousness is cooperative."

"The soul and ones consciousness are one with the flesh so long as the flesh lives," Kiel said. He knew the dynamics of that very well given who he was. "And Unit 01 was made from the living flesh of the Second Angel. She may have been essentially inert but she was still indeed alive. Even with her soul, or the bulk of it transferred to another being..." He indeed knew what Rei was and always had... "enough of Lilith's consciousness remained to transfer itself to the flesh utilized to make Unit 01."

"And like all other Evangelions that consciousness was indeed bestial," she continued. "How could it not be given the damage we did to her flesh? She may have been inert but she was still aware and she could still feel. We ripped her body apart and Gendo tore apart her soul. She could have easily tore my soul apart yet she didn't. I think she instinctively understood why I allowed myself to be taken into the core. Over time through our interactions she began to regain herself but her memories and experiences remained fragmented until the attack of the Fifteenth brought them all back to the surface. She remembered you as someone who had been on this world for a very long time but it wasn't until her memories returned that she remembered exactly who and what you are."

Kiel remained silent for a moment before doing something that surprised everyone in the room. In a low and subtle manner, he began to laugh. "Of all the multitude of things I have contemplated and planned for all this time, _that_ was definitely not one of them. However, it will not matter. You have gained knowledge but nothing else. She is restricted in that form, a mere shadow of her true self. The last and strongest of Adam's children is within the seventh mass production unit. She is no match for him. You have sent your son to his doom Dr. Ikari."

"It sickens me that I have to send him out there at all," she said. "But I would never send him into a fight he cannot win. I'm not Gendo. I'm not looking to manipulate him for the sake of some ridiculous scenario." She turned and looked at the screen as Unit 01 made its arrival. "Whether she is strong enough in this form or not, and I am sure that she most certainly is, we still have a weapon in our possession that I can send to them in an instant if they should need it. Push of a button and it's there."

"The Lance," Kiel growled. He gestured to the console she had been sitting at. "Dr. Holzer, if you would." Even if he did not necessarily need the Lance for his scenario, it would be to his advantage to make sure they couldn't utilize it.

With a sneer Holzer went to step past Yui. She pulled her hand out of the right pocket of her lab coat producing a taser, the same one she had zapped Gendo with, and jammed it into the soft flesh under the German scientist's chin. He made a peculiar screeching sound and danced about on his tip toes for a few seconds. As he hit the floor Kiel's top bodyguard Josef turned his gun on her and opened fire.

* * *

 _ **Topside**_

Unit's 00 and 02 knelt down and released their entry plugs as Unit 01 stood watch, Rei and Asuka riding the emergency ladders down to within a few feet of the ground. Rei had no problem but with one bad foot Asuka made a less than graceful landing, stumbling and coming down hard on her butt. The jolt didn't do much good for the cut down her back.

"Are you alright?" Rei asked, looking at the redhead's wounds.

"Yeah," Asuka answered. "They hurt but it's not that bad. What about you?"

"The same," the bluenette answered. They watched as a headless MP unit charged at Unit 01 only to be met with a kick that sent it tumbling away. Another with a smashed in mouth swung its lance only for it to be stopped dead by Unit 01's AT field.

"They cut right through mine!" Asuka exclaimed.

"Mine as well," Rei admitted.

"How is Unit 01 strong enough to stop them?" Asuka asked.

"Rei! Asuka!" Shinji's voice came over purple Eva's exterior speakers, saving Rei from answering. "You need to hurry and get in the plug with me!" As he said it Unit 01 went to one knee like their units and extended its entry plug.

"That's not possible!" Asuka yelled. "How can he maintain an AT field with his plug ejected?!"  
"Unit 01 is special, different from all other Evangelions," Rei answered cryptically. "You will soon find out why."

"Is this another of those secrets you told me NERV was so full of?" Asuka asked.

"It is," Rei answered. "But even the Commander was not aware of Unit 01's true nature until shortly before he died."

She wanted to know those secrets but she was beginning to fear just exactly what they would entail. She sighed. "So how do I get up there? I can't climb with my foot as it is and the ladder won't retract with me on it so I can't ride up."

Rei regarded her for a moment. "I will carry you."

"What?! You can't climb up there carrying me!"

"I will not have to climb."

Startling the redhead, she easily picked her up in a bridal carry. Asuka was about to protest when she turned ashen white and became speechless when wings made of orange light similar to Unit 01's came out of Rei's back and spread out around them.

"Y-you're an A-Angel?!" The words were little more than a whisper and the girl was trembling.

Rei cocked her head to the side. "Perhaps. Perhaps not. I am a clone made by Commander Ikari from the DNA of the Second Angel and a human donor. My Angelic make up has since subsumed the human part. I do not know how I would be classified but I have not sought to define myself as anything other than Rei Ayanami. I am me, regardless of my genetics."

Despite her explanation, or perhaps because of it, Asuka was essentially locked up in fear. She was breathing quickly and her eyes were wide. Her trembling turned to outright shaking. Her already strained and battered mind was trying to decide if she should fight or flee and the idea of fleeing was winning out.

Rei looked directly into her eyes. "I am no different now than I was when I came to the hospital to see you this morning," she said. "I am no different now than I was a few minutes ago when we were fighting side by side. There is no reason for you to fear me... unless you harm Shinji and then I would suggest that you should be very afraid of me."

With that she took flight and made the short trip up to Unit 01's entry plug, dropping Asuka in with a splash and a resulting indignant squawk that brought the girl out of her shock, before joining her and closing the plug's hatch. Immediately the plug moved back into position and refilled.

"You're both hurt!" The worry was evident in Shinji's voice.

Asuka scrambled over to him. "Shinji!...Rei...she's..."

"I know Asuka," he said calmly and with a slight smile. Boldly for him he took Asuka's trembling hand in his. "It's alright. I was a mess too when I first found out but I finally realized that it doesn't matter how she came to be or what she is. She's still Rei and I still care about her no matter what." He averted his eyes and his voice became quieter. "J-just like I care about you too even after everything that's happened."

She was stunned. The boy she had always seen as meek and who her other half had always labelled as a coward, had just been bold enough to take her hand, try and reassure her...and admitted that he cared about her. And the way he had looked at Rei...

He stopped and seemed to be listening to something she couldn't hear. His face turned red. "Misato!" he exclaimed softly. His face seemed to turn even redder and it was a wonder that the LCL around him hadn't started to boil. "I am not trying to add to my harem!" he hissed. "I don't have a harem...stop it!"

"He is in denial," Rei deadpanned.

Asuka blinked. _'What...what in the hell is going on?!'_ "The whole freaking world has turned itself inside out while I was gone," she muttered.

"Ugh!" Shinji groaned. "Fine. I have a harem and you're at the front of the line...Of course I love you Misato, do you think I could take all the teasing if I didn't?"

Asuka blinked in disbelief again. _"What?"_

"What?! I know we have other things to do right now...but you started this!" He sighed and chuckled lightly. "I see what you're doing now Misato...and thank you. I needed the distraction."

Seeing the puzzled look on Asuka's face, Rei spoke up. "He has been worried since he launched," she explained, telling half of the truth. Asuka didn't need to know what happened in the cage after they left. "In her own way Misato was easing his mind."

"We all need to sync with Unit 01 now," Shinji announced.

"You and I synced with Unit 02," Asuka said, still a bit shaky. "But is it even possible for three people to sync with an Eva?"

"It will not be a problem," Rei answered. "Just concentrate as you usually would but be prepared, we will be synchronizing far deeper than you ever have before."

"Don't worry," Shinji assured her. "It'll be okay."

She tried to calm herself as much as she could and concentrate on synchronizing, if anything it would distract her from her fears and the revelations of the last few minutes. But she was still pretty rattled and feeling even more like she had entered an entirely different world after leaving her hospital ward. She was seriously beginning to wonder if her mind hadn't created a parallel universe in her head as a way to cope with the fallout of her breakdown, and even things in it were going sideways. Was any of what was happening even real? When Shinji had come to visit her she had told him that nothing felt the same, that maybe it was because who she was now felt the world differently than her old self. Was that true or was this world she was in not actually real and just existed inside her own head? Had she truly gone insane and lost herself?

"You are damaged but not broken little one," a soft yet powerful voice said. "And this world you are experiencing is indeed real and the same one you knew before."

She opened her eyes to see a mass of slowly swirling colours, much like in the start up sequence of her Eva. She was in the midst of it, seemingly floating weightless in mid air. The second thing she saw was a tall, dark skinned woman with long dark hair and green eyes, gently smiling at her. She was naked.

"Even if this world isn't real I wouldn't care," she heard Misato say. "Because I get to do this!"

She turned in time to see an also naked Misato jump onto Shinji's back and wrap her arms around him. He was naked too... _completely_ naked she noted as she looked downward and her face turned a brilliant shade of red and her eyes widened. She realized that his face was red as well about half a second before she also realized that she was just as naked as everyone else.

She screamed and practically curled into a ball. "Why are we naked?!"

"It is the natural state of the soul," Rei's soft voice answered as if it should be obvious. Really, she didn't see what the big deal was.

"It's very liberating once you accept it and accept yourself," Misato chimed in. "That can take a little time though but it's definitely worth it. So how are you holding up kiddo?"

"I...things are...upside down and inside out," she said shakily. "Nothing's the same. I feel like a piece that doesn't fit but I'm afraid to find out the truth that it seems I obviously don't know."

"You were used and manipulated just like everyone else," Lilith said. "That alone is hard to accept and the reasons for it will be hard to hear. But you will hear it. We will make sure that you know the truth and we will help you deal with it."

"Who are you?" Asuka asked.

Lilith smiled. "For now, suffice it to say that I am Shogoki. Anything more will have to wait until we defeat the Seventeenth, because if we don't then nothing will matter. We, all of us together will defeat it and put an end to this long nightmare."

"But how?" Asuka asked.

"I can balance the synchronization of all of our minds," Lilith answered. "Each of you have specific skills that will blend together. You are a natural and skilled combatant. Misato is also a skilled combatant and has a mind for tactics. Rei displays calmness, patience and steadiness. I supply the power, and Shinji is our backbone. He is someone we all believe in and has a strength that he does not even realize but which comes through when needed. The Seventeenth, no matter what kind of an enslaved abomination Kiel has made of it, will not defeat us."

The colours swirling around them intensified and became brighter. Asuka felt a pull much like what one experienced during initial synchronization only more intense. It was a weird sensation. She had synced at a very minor level with Unit 01 before so that part of it was known. But there was another feeling, a very odd one that she instinctively knew must be the minds of the others around her. It was like she was becoming one entity with them and then they were all becoming one entity with the Eva. She was on the verge of panic before she realized that she could still feel herself as an individual and that she wasn't being assimilated somehow. It was still scary though. It was like she was a part of them and they were a part of her and they were all becoming the Eva. On the periphery of her mind she could feel familiar things about them that she knew to be traits of their personalities. Except for Shogoki of course but she did get some sense of a motherly feel from her. It was fierce and powerful, but still motherly none the less.

Over all it was an expansion of self unlike anything she had ever experienced before. Synced like this they were all the soul of the Eva now.

Outside, Unit 01 dropped its AT field and with the resistance gone the unit with the smashed mouth that had been wailing at it stumbled forward. Grabbing the right arm which was holding the double bladed lance, Shogoki twisted it and jerked it savagely, breaking the arm at the elbow. Another twist and pull and the joint came apart. Using its left hand Shogoki took the weapon away from the MPE and used it to cut its wounded arm off at the shoulder. Undeterred the MPE turned back to attack again. Switching the blade to its right hand Shogoki sheared though its neck at the shoulders, then quickly raised the blade and lopped off its other arm before kicking the unit away.

The other damaged unit still standing came rushing in from behind and was met with a perfectly executed and devastating back spin kick that crushed the MPE's chest armour and sent it flying into a row of decrepit apartment buildings, bringing two of them down and leaving the enemy unit embedded in a third.

Somewhere within Unit 01 Rei felt rather joyful at seeing her old dwelling reduced to a pile of rubble.

Turning back to the now armless unit a quick swipe of the blade took off its legs leaving it totally immobile. A downward strike bisected it, cleaving it in two and destroying the plug and the core. For whatever reason that was the moment when the last unit containing the Seventeenth decided to attack.

Shogoki met the swing of its blade with its own, a resounding clang booming across the empty city. Again and again the blades clashed, the sound ringing off of the mountains around the city and creating a near constant din. The movements of this unit were a little sharper and more precise that the others, but not by much. It definitely seemed more powerful but its coordination still seemed sort of...zombie like and it seemed to drool worse than the other units. Lilith knew the names of all of Adam's children and the titles that came with them. If the movements of Tabris within this mass production unit were true and not a ruse of some sort, then it seemed that Kiel had somehow cancelled out the Angel of Free Will's ability to act on its own accord.

Perhaps the destruction of her old body and the resulting end of the Call that Adam's children had been following to Tokyo 3 played a part in it, but it would take more than that to turn the most powerful and intelligent of Adam's progeny into this near shambling abomination. It seemed to operate on instinct and little else.

The clash of blades had fallen into a pattern and Shogoki took advantage of it. Rather than continuing to block the next strike she sidestepped it and brought her blade up and severed the MPE's right arm just above the wrist, then followed with a downward backhanded strike the bit deep into the unit's right shoulder. Surprisingly the unit snapped at her face with its jaws causing her to tilt her head back, then followed with a left handed punch to the chest that made her stumble back a couple of steps. Rather than follow up it retrieved its weapon with its left hand. Shogoki took the opening and attacked, forcing the Seventeenth onto the defensive.

It blocked as it gave ground but she kept forcing the attack. A hard strike drove the Angel's blade far enough out of the way that it couldn't block the quick follow up aimed at its core but it surprised her by throwing up an AT field, something the other units hadn't been able to do. Just as she began to pull back it dropped the field and stabbed its lance forward, scoring a wound down her right side. It hurt, bad. They all felt it since they were for all intents and purposes a single entity at the moment. Despite the pain she countered immediately, driving her left fist into the MPE's already wounded right shoulder, the blow practically exploding the joint. As she went to strike again the MPE deployed its wings, batting her off balance with one and giving it enough time to jump up and take to the air.

Two could play at that gave. Deploying her AT field as wings again, Shogoki took to the sky after it and it soon became clear that she had an advantage. She could use her AT field to propel herself at faster speeds where the MPE seemed restricted to beating its wings like a bird to gain speed. It either chose not to use its AT field in the same way or it could not do so. Also, with only one good arm and hand to wield its weapon with, its right side was a vulnerable target. As it was it was capable of a fair amount of speed and could execute some quick dips and turns but it couldn't make tight turns.

For Shogoki using its AT field was more like defying gravity than actual flight and that gave her the ability to move quickly and sharply in any direction or even remain still in mid air if she chose. They dove and swooped at each other and clashed several times before she was able to manoeuvre into an opening to strike the right side. When she did she cut the right wing in half, sending the MPE spiralling into a crash landing several hundred feet below.

When she was touching down again it was just standing back up. Much of its armour was cracked and broken and one leg was badly damaged. There was also a large patch of flesh torn out of the left side of its long neck. The damaged beast raised its head and emitted a loud, wailing screech and without warning it fired a cross flare that sent her slamming through the rest of the row of decrepit buildings it had tossed another MPE into earlier. First the AT field, now this. If there had been any doubt at all before that the Seventeenth Angel was within that unit it was gone now.

It wasn't done with the surprises however. Beneath its broken armour the flesh seemed to be moving. It shifted and bulged and in places began to push out between the cracks in the armour. The right shoulder swelled, seemingly repairing itself and the arm began to stretch. It snaked out across the ground until it came into contact with the MPE with the broken back, which was trying to pull itself around by its arms. The arm retracted like an overstretched rubber band, dragging the wounded unit with it. The left arm did the same thing, ensnaring the other unit that had lost its legs but was still otherwise functional.

While it was doing this the remaining functional unit that Shogoki had smashed into the row of buildings it was now in the midst of, rose up and faced the purple Eva looking to resume the fight. It wasn't to be however as the two arms of the Seventeenth stretched to grab it and drag it back as well. What happened next was as fascinating as it was grotesque.

An AT field formed around the MPE body of the Seventeenth as its flesh continued to shift and bulge. The unit screeched again as armour plates popped and erupted outward and tendrils of flesh ensnared the remains of the other three MPE's it had drug to itself, digging into them and pulling them in closer. From all four units came the sickening sounds of cracking armour, popping joints, the ripping of flesh and the cracking and snapping bones. Blood squelched and squirted all around it but seemed to be sucked back into the writhing, shifting, nightmare mass of flesh. There were sparks and small flares of energy as the four cores ground and scraped against one another as they settled in the middle of the roiling mass.

After several minutes the body began to take on a more coherent shape. With the same eerie symphony of sound as when it began, flesh and bones finished changing shapes and forming new joints. Taller and wider now it was supported by six legs. Three arms sprouted and grew out of each side and two more came out of the back at shoulder level. One fully formed head and neck rose from between its shoulders with a bloody stump of another on either side of it which were beginning to regenerate into duplicates. A fourth long head and neck protruded from its chest. Random broken pieces of armour covered the body in a haphazard fashion, a concentration of which protected the four cores in the centre of its torso and portions of the entry plugs stuck out around them. The unit was now easily three times its original size.

Shogoki could only watch, unable to do anything about it. The AT field the Seventeenth was generating to protect itself and perform this melding was not something she could break through, at least not easily or soon enough to stop it. In order to put that field up and go through that level of transformation in such a short time, the Seventeenth must have nearly maxed out its own S2 as well as the artificial ones of its own MPE and the three it collected.

Lilith could feel the revulsion and the fears of the others. To be honest she had reservations herself. She had no idea what she could really do now in Unit 01, its limits and capabilities had not been tested since it acquired and assimilated the S2 organ of the Fourteenth. It was going to take a great deal of power to fight this thing and hope to do any significant damage. She assumed that the grotesque amalgamation would be able to regenerate any damage they could inflict upon any part of it with the exception of the cores.

They would also have to be very careful about not letting their enemy get a grip on them. If it did it could assimilate them too and if that happened it would bring about Third Impact. That made the fight that much tougher since they needed to try and stay out of its reach, yet they had to be close in order to destroy the cores and hack their way to the plug containing the Angel. They would have to find a way to get the job done.

The AT field around the Seventeenth faded and the thing rose up to its full height. The arms quivered and jerked and the drooling heads lolled about independently. The arms suddenly stretched out all around it an collected the remaining six lances, the top and bottom set of arms as well as those on the back each holding one. The heads all raised and emitted a loud screech, issuing a challenge to battle. Shogoki rose to its feet, shattered its jaw restraints and defiantly roared back in answer.

* * *

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And while you're here, check out my other stories.


	34. Chapter 34

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

3 chapters left after this one.

 **Transposed**

 _ **Chapter 34**_

The staff on the bridge shrieked and hit the floor when Josef opened fire. In the dead silence a moment later when they raised their heads back up they expected to see Yui lying on the floor in a pool of blood and not the sight they were greeted with instead. She was alive and well and in front of her was a field of orange hexagons. Those who were not fully aware of everything were shocked, some horrified, and all were stunned. The ones who were aware, like Fuyutsuki, Kaji, Maya and Ritsuko were surprised but not in a state of shock.

"She has to let me test her out on _that_!" Ritsuko whispered in a voice that only Maya heard. The tech nearly giggled over it.

"I see," Kiel said gravely. "Your level of contact and interaction with Lilith has led you to this. You won't be able to hold it for much longer, I can already see the strain on your face from trying to maintain it."

"You might be surprised how long I can hold it," she said. "Survival is a great catalyst."

"Yes it is," he agreed. "But your body will give out long before your will to survive will and when that field drops Josef will put an end to you."

"Yeah, I don't think that's gonna happen you old geezer," a young female voice said from off to his right.

Before anyone could react four tendrils of orange light impaled each of Kiel's bodyguards through the head, killing them instantly. As the tendrils retracted and the dead men dropped to the floor, everyone's eyes followed them back to their source which was the upraised right hand and wiggling fingers of a teenage girl who was leaning against the wall of one of the MAGI modules. The well endowed girl was dressed in a white Oxford shirt with a dark green tie worn out over a red and green plaid skirt, black thigh high stockings and brown loafers. She had a crooked, mischievous grin on her face that was reflected in her green eyes behind the lenses of a pair of oval, red framed glasses. Her brown hair fell to the middle of her back and was gathered into twin tails.

"A little raw and rough but an impressive display Shinj's Mom," the girl said with a cheeky grin. "But you might want to stop now before you hurt yourself."

Yui was glad to comply and dropped her AT field. Her legs gave out and she wilted to her knees then slumped back onto her butt. She felt utterly spent, she was sweating and she felt like every inch of her body just under her skin was on fire.

"Yui!" Ritsuko exclaimed, rushing over to her.

"She'll be okay," the girl said, her tone unworried. "First couple of times it knocks the heck out of you and you feel like you've got liquid fire flowing under your skin. Once you get used to it you just feel tingly all over. Kind of nice really."

"Who are you?" Kiel growled icily. "And how did you get in here?"

"Don't tell me that you've forgotten me," she said, her voice icily sarcastic. "Of course I suppose you can't see too well with that visor. Did you get that idea from Star Trek? Got news for you gramps, you're no Geordi La Forge." She shrugged. "Maybe you're just old and forgetful."

Kiel's face was getting redder by the moment and the armrests of his wheelchair were creaking under his straining grip. "I will not ask you again child."

"Or what, you'll glare at me until I get sick of you?" she sassed. "Sorry, already there you senile old goat and in case you've lost your short term memory you have nothing to threaten me with. Your bodyguards are dead, Holzer is unconscious and useless even if he wasn't, and I know you aren't armed."

She pushed off from the wall and stepped closer to them. She addressed herself to Yui and the others rather than Kiel. "My name is Mari _Illustrious_ Makinami," she said cheerfully and with a slight bow. "Nice to meet you all and _finally_ allow myself to be seen. She turned and settled a cold gaze on Kiel. "But this genocidal old fart knows me by a different name. To him I'm Experimental Subject 77707."

Kiel flinched in his chair like he had been slapped. Another impossibility had just presented itself to him and it hit him harder than the others. Part of it was due to how long he had tried and the number of test subjects he had gone through to get his desired results, which he was never able to accomplish. The fact that she was standing before him right now meant that either someone had found a way to stabilize her genetics, which he didn't believe to be the case, or they had isolated and split her combined genetic make up back into one of the two contributing matrices. The other thing that was hitting him hard over her presence was that if she was here, then someone sent her here and that did not bode well for his plans.

Before he could speak, Yui did. "You were part of his experiment to combine the traits of the two different Seeds."

"Yup," Mari confirmed. "One of many and one of the few to survive even while in stasis. Old fart couldn't even get that right." She pinned him again with her gaze. "Do you have any idea what it's like to know and feel nothing else but pain you old bastard? Your stasis didn't put us into a complete state of suspended animation, it acted like a massive slowing of time and we felt all the pain associated with our bodies breaking down over the span of _hundreds_ of years and we had no way to escape it or make it stop. Some went mad and their brainwaves flat lined. They were the lucky ones because they could no longer feel or sense anything at all until they died. Some had their bodies slowly fall apart, others exploded when their partially formed S2 organs collapsed. Others like me suffered until they were found and placed in proper stasis and then helped."

"I thought his race was one that was supposed to value life as something precious?" Ritsuko asked as she kept an eye on Maya who looked like she was going to be sick.

"Most of them do," Mari answered. "But he never considered us as 'lives'. We were experimental tissue grown in a lab for the sole purpose of his experiments. We were expendable."

"Most of them are fools," Kiel spat. "Still stuck in their ever repeating cycles of ridiculous moral and existential evolution. They seed worlds then abandon the life forms that evolve. They offer them no guidance or protection. They allow them to suffer and tear themselves apart like animals or fall prey to other races."

"And you decided to throw morals completely out the window with your experiments," Mari spat. "Long ago you and your kind chose to remain in physical forms rather than become beings of pure thought or energy so that you could better experience the wonders of life and evolution in all of its near infinite methods. A decision that all of the First Ancestral Race deemed to be the greatest way they could honour their belief and commitment to the sanctity of life. Yet you created life and made it suffer for the sake of a point of view you couldn't force into reality."

"Do not dare to preach to me child," he said angrily. "I argued and debated the issue for millennia long before you were a culture in a lab dish. My race has gone through eons where they are the most arrogant and selfish of creatures, to eons where they rediscovered their moral compass and compassion. It is a timeless exercise in our continuing evolution where we continue to learn as much about ourselves as we do the other races in the universe. That is the bane of our own evolution. Yet one thing has always remained constant. The edict of non interference that has seen untold billions suffer and die because we would not give them the slightest bit of aid or the tools to thrive and survive peacefully or even the power to protect themselves. _'In all things they must evolve on their own and in their own time as we did ourselves'._ It is a weak argument that absolves us of all blame for their fate. We brought them to existence, therefore we have an obligation to nurture them."

"What help did you give us?" she asked angrily. "We were nothing more than the few eggs you had to break to make an omelette. A small and insignificant price to be paid to prove your point. Just like the billions you've killed here and the billions more you want to kill are an insignificant price to pay so you can restore yourself, escape your punishment, and go back to your obsessive experiments."

"If they will not see reason and accept what they must know to be true, then the only way to change the situation is to create a better Seed with the traits of both the Fruit of Life and the Fruit of Knowledge," he said with absolute conviction. "If they as a whole will not take responsibility and change their ways, then I will do whatever I can to give the lives we create a better chance to survive. Maybe then they will see the value in guiding those creations."

"Your actions don't match your words Kiel," she snarled. "You are nothing but a hypocrite, the largest the universe has ever seen."

"You are the stereotype of a mad scientist," Yui said. "You will go to any lengths to prove your theories or to remain free to do so, no matter how hideous the cost is and you will always find ways to try and justify it."

"And how are you any different Ikari?" he sneered. "You spoke of the pain Lilith underwent but you were responsible for a great deal of it, all so you could create the Evangelion. Then you manipulated your own precious son into the pilot's seat knowing full well the pain he would have to endure, all in the name of a scenario you now consider evil and which you once believed wholeheartedly in."

"You're right," she agreed. "I did, and I will spend the rest of my days trying to atone for that. But I came to my senses and realized just how wrong I was and I have no problem in admitting that. I was naive and stupid and blinded by the wonder of the things I was accomplishing."

"But you couldn't do that, could you old man?" Mari said. "You had thousands of years to reflect on what you had done, to find ways to help the people of this world in your capacity as one of them. You may not have had your power, but you still had your mind, your intelligence, and your experience. You could have set so many things in motion that would have made a difference. Instead from the very beginning of your time here you schemed to escape your punishment and regain your power. You had the chance to do exactly what you've been fighting for."

"How naive," he huffed. "You think that anything I would have been able to do as one of them would have accomplished anything tangible? You're a fool if you believe that. Wars would still have been fought and killed millions. The strong would still prey on the weak, and those with power and influence would still use and abuse those that they governed. Even if I was sent here in my true state it would have required several of us with a coherent plan of action insinuating ourselves into the earliest days of civilization to push the people of this world onto a better path."

Mari snorted derisively. "If you hadn't been so buried in your research and doing foolish things to earn your exile then you would have seen that things were changing, that your peers were beginning to see the merits of being more involved and were slowly beginning to do so. Some are living out lives on seeded worlds and involving themselves in ways than can make an impact on those worlds. Others are becoming involved early on and helping to guide growing civilizations. You'd be surprised how much has changed since you've been here."

"Like you?" he asked, shifting the subject. "Who was your great saviour and which side of your genetics did they remove in order to stabilize you?"

"You think they..." She began to laugh. "You're so arrogant that you think no one else could do what you couldn't? You do realize that you weren't the only one working on that right? You were just the one using the most unacceptable methods."

"Gosche." Kiel said sourly. "I am well aware that he was conducting research in the same area but his methods were ponderous at best and progress was so slow as to be virtually nonexistent."

"And yet he accomplished what you couldn't," she jabbed. "At the very least he was able to fix your failures and he didn't do it by removing the genetics of one side or the other." She grinned maliciously at him. "He did it by introducing a third element to balance the other two."

"Preposterous!" he exclaimed. "There is no element short of our own genetics that possibly could do such a thing and that is forbidden. Gosche wouldn't have the stomach to dare...even I would not go against _that_ edict."

"Well you are correct about that much," she agreed. "He would never do that, but you are very wrong about there not being another stabilizing element. Maybe the senility had already begun to set in back then and you forgot all about the properties of the Lance?"

"Ridiculous," he scoffed. "The Lance is inherently more powerful than a Seed, practically poison to it. That's why they are sent out with each Seed to act as a control and fail safe mechanism should the Seed exceed the parameters of its role."

"They also have a certain level of sentience of their own that allows them to determine when or if they need to act," Mari explained for the benefit of the others. "Did you forget that Gosche was the one who was most responsible for the creation of the Lance's in the first place? If there is anyone who knows how they work and how the technology can be utilized in other ways, it's him. He used the properties of the Lance to stabilize our genetics and save our lives. He gave us a chance to be something other than your failed and forgotten experiments." She grinned savagely at him. "I can tell by the look on your face that you don't believe it but I can assure you it's true. _'If Adam is the Fruit of Life and Lilith is the Fruit of Knowledge, then the Lance is the scale that balances them'._ That's how he described it and it doesn't matter if we're talking about a Seed or an Angel the size of a skyscraper or a girl the size of me. It's all the same."

Kiel was dumbfounded. He had been positive that the secret to making the two genetic structures that were so opposed to one another work lay within them and not with a third element. The genetics of the Seeds were unbelievably and incredibly complex on their own and trying to integrate a third element into that was something he thought to be virtually impossible. Trying to make that show even the slightest of results would have taken a prohibitively long time and may well have never reached a stage where it would be worth pursuing further. Yet, evidently there was evidence to the contrary right before him.

And what of her? He knew potentially how powerful she could be with the genetic make up of the two Seeds, but did the properties of the Lance increase that? Did it negate them and simply balance her? She clearly had some level of power in order to be able to manipulate her AT field the way she had. And why had she been sent here?

"My god...what the hell is it doing?!" the panicky voice of Makoto Hyuga cut into his thoughts. Up on the giant view screen the MPE containing the Seventeenth Angel was undergoing its metamorphosis. Kiel couldn't help but grin when he saw it. It wasn't going to matter what was inside Unit 01, it was not going to stand against what the Seventeenth had done to itself.

"Your Viagra just kick in old man?" Mari asked with a crooked grin. "Because getting a hard on at your age would be the only reason you'd have to smile right now."

He ignored her crude insult. "You seem to be overestimating what Unit 01 will be able to do against the Seventeenth now."

"You're welcome to your delusions you old fossil," she said. "Because that's all you have left. Unit 01 is more than capable of defeating it and even if it doesn't you'll still lose. That's why I'm here. Why do you think I've spent the last ten years shadowing every move you and your Old Farts Club at SEELE has made?"

"You've been here for ten years?" Ritsuko asked incredulously.

"Second Impact didn't go unnoticed," she began, turning a glare on Kiel again for a moment. "Just because no one came after you then doesn't mean they didn't notice." She turned back to the others. "I was sent to see what happened and it took me two years to put everything together, to figure out what happened, how and why it happened, and who was responsible for it. I wanted to put and end to this fool right then and seek out and end Adam's children before they could awaken but I wasn't allowed to. By that time mankind had begun to develop a way to fight them. You had survived the cataclysm and found a way to fight for your survival and I was instructed to allow you to try and only intervene if it looked like Kiel was going to get his way and initiate Third Impact."

"Y-you could have stopped all of this a long time ago?" Maya asked shakily, her face turning an unhealthy shade of white.

Mari's expression sagged. "Yeah, I could have and I wish upon my very life that I had been allowed to do so. Every time I had contact with my mentor to report in I begged and pleaded to be able to put an end to this but I wasn't allowed to. So I kept watch. I shadowed members of SEELE and NERV. I read a lot of computer screens over people's shoulders and stole a lot of passwords and spent countless hours snooping out what was going on. I accumulated every bit of information I could from as far back as I could and right up to the minute. I hoped that with every scrap of information I could put together about what Kiel had done and was doing that I could get them to let me stop it before it got to this point."

"But they wouldn't let you," Yui said gently. She wasn't exactly happy about it but she could understand why it had been this way. After regaining all of her old memories Lilith had told her a great deal about how the First Ancestral race thought and went about things. They went to great lengths to avoid acting like God to the races they spawned but by doing so they left themselves open for people like Kiel or even the evolved races from some of their earliest seedings to try and interfere in various ways and abuse the system.

"They gave you the task of being an enforcer but because we found a way to fight for our survival they wouldn't let you do your job."

"Yeah," sighed. "I hate it. Not the enforcer part to if, I like that. I believe that the bad guys deserve what they have coming to them because they chose to be that way. I hate it because I know what it is to suffer. Even after I was saved it wasn't easy. I had no identity and as I struggled to find one I didn't know how much of it was mine and how much was influenced from the genetics that made me what I was. I didn't even have a name until I came here. I just went by 'Seven'. It reminded me of how I began. Gosche wanted to give me a name but I felt like I had to earn one, that I couldn't have a real name until I found myself. By the time I was ready to come here I had done that and during that first two years I came up with a name that just felt right to me. I had finally found myself and I liked what I found, but how could I be happy when I saw so many who weren't?

As my self imposed punishment for not being allowed to stop any of it I followed people around and bore witness to that misery. I had hopes and dreams about staying on this world after my job was done but I didn't deserve to think about it when so many other people were suffering for my forced inaction. The one who's misery hit me the hardest was Shinji's. He was a lot like I used to be and felt like I used to feel a lot of the time."

There was something in her voice and in her eyes. "You've watched him for a lot of his life haven't you?" Yui asked.

She nodded. "When I learned what happened to you and that he saw it, and when I learned that Gendo just left him at the train station for someone to pick up, I decided to keep track of him as much as I could," she answered softly. "So many times I wanted to allow him to see me, to give him a friend and someone who would care about him even if I was the only one. Since I couldn't do that I just hung around him when I could, talked to him and acted like he knew I was around." She wasn't about to tell her how she sometimes used to do that. "Kind of selfish I know, since I'm the only one who got any benefit from it."

Yui smiled lightly. "Well, even if that's the case and even if he didn't know you were there, at least he wasn't as alone as it seemed."

"Such sentiment," Kiel snorted. "Enjoy it while you can, this will be over before long and I will be restored no matter what you think you can do to stop it."

A streamer of orange, originating from the middle finger of Mari's left hand, shot past the right side of his head, slicing off the push handle on that side of his wheelchair. "Here's an idea, how be you just shut your mouth before I remove it...along with your head. You seem to think you can still have your way."

"I do," he said, seeming to regain his earlier smug confidence. "There are too many minds and souls trying to work together inside that Evangelion for it to ever be effective against the Seventeenth, especially as it is now. And I sincerely doubt that you have the power to stop it yourself, no matter what you claim to be."

"Old geezer, you've crapped out on every other objective you set for today and I don't see that losing streak ending," she said coldly. "I am really going to enjoy watching the look on your face as you see it all swirl down the drain."

"I can say the same of you," he countered. "We shall soon find out who is right."

He put his doubts out of his mind. He had worked too long and too hard to get to this day, carefully orchestrating things to get him to this moment. Yes, not everything had gone his way today or in the recent past but he had been able to adapt and stay the course. Yes, his replacement army of mercenaries had failed to keep the pilots from their Evangelions. Yes, he was short two MPE's but the remainder, while not destroying Unit's 00 and 02, had run them out of power and taken them out of the fight. Now their pilots, one of whom had a fractured mind, were trying to pilot Unit 01 together, an undertaking that was sure to fail no matter what they had been able to do thus far.

There was no scenario that had ever seen him accounting for Lilith being the Eva itself but it wouldn't matter if she indeed was. Even if she had enough power in this form, she would still be tied to the minds of the Children trying to pilot her and that was more than enough of a handicap to all but ensure his victory. This had to work and go his way. No other outcome was acceptable.

* * *

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	35. Chapter 35

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

Third to last chapter

 **Transposed**

 _ **Chapter 35**_

Charging straight at the monstrous MPE probably wasn't the most sound idea, but they needed to know what it could do and how it fought in order to find a way to defeat it and straight ahead was as good a way to start as any. Trying to come around at it from the side showed them that the ungainly looking unit could actually move pretty well on its six legs. The bottom four arms were within their height and reach but the top two could strike down at them and would require them to jump or take to the air to remove that advantage. Also, a frontal attack meant their one lance facing four. No matter though, they still had to feel out their opponent to gauge the best way to fight them and until they could get some assistance from the bridge and get their hands on the Lance, they had to find another way.

On the first attack the MPE blocked their blade strike with its top two blades and tried to gut them with swipes from the bottom two. They jumped back quickly but still received a shallow cut to either side, showing them that despite the way it looked their opponent was capable of swift and reflexive action and they would have to keep that in mind. Straight on obviously wasn't going to work so the next attack saw them veer to their left at the last moment which kept them away from the arms on the MPE's left side. The lower right arm blocked their swing and they had to spin out of the arc of a swipe from the upper arm. They were able to land a backhanded swipe across two of the legs but got a slice down the back of their right shoulder from the arm on the right side of the MPE's back.

Putting some space between them, they watched as the wounds they had inflicted on the legs quickly healed themselves. It seemed that they would need to do a great deal more damage to affect it and find a different method of attack since the multiple sets of arms covered the gaps created when the others were in action. Two attacks and three wounds taken could attest to that and that was not a favourable ratio for them. The best chance to counter that and change their effectiveness was to use speed. While the MPE seemed to be able to move well enough, there was no way it was faster than they were.

They came at it fast, striking or blocking but avoiding a follow up strike from one of the other arms. Shogoki's armoured feet tore up the asphalt and concrete and buckled metal plates as they dug into make sudden changes in direction and as they hopped and jumped around. The speed kept them from taking more wounds but they were unable to inflict any damage in return. Several minutes of this tactic only succeeded in tearing up the ground and making the footing bad, which caught up to them when the churned up surface gave way under them and caused their right foot to slide too far and sent them to the ground.

The Angel took advantage immediately, moving in on them and striking with its blades as they tried to get up. A hard, sweeping slice from their own blade deflected both of those wielded by the lower set of arms, while a spinning leg whip caught and broke the right front leg causing the the Angel to unbalance for a moment. Rising into a crouch they sought to sprint out of the thing's reach but it was ready for them. The top two arms stretched well out in front of them, slamming their blades into the ground and blocking their path while the two middle arms stretched out and caught them by the right ankle and left arm and started to pull them back.

Pulling hard with their left arm and twisting to the right they were able to resist some of the pull while also severing the lower right arm as it came up in an attempt to stab them. They couldn't avoid the lower left arm however and it sunk its blade into their left side and the head sticking out of the MPE's chest locked onto their left shoulder and tried to bite through the armour. They howled in pain and pulled and twisted harder against their enemy's grip and were able to also sever the arm holding their ankle. Luck was with them at least in part as they dropped toward the ground and the two upper arms which had been retracting and looking to skewer them missed their target.

Twisting back to their right they blocked another stab by the lower left arm. The middle arm gave a savage twist and broke their left arm. With the upper arms moving to try striking at them again, the lower left arm recoiling for another try, and the middle arm and the chest mounted head still refusing to let go, Lilith pulled out a trick of her own that she had been saving for later and in case they got into a bad spot. This certainly qualified. Turning their gaze on the enemy their eyes glowed and a cross flare bloomed between them and the MPE Angel, the force of it pushing the two of them well apart.

Getting back onto one knee they waited for the dust and debris to clear so they could see how much damage they had done to the enemy. The cross flare hadn't been at full power but wasn't weak either and it had been sufficient to get them out of a tight spot without taking any more damage. As it was the wound to their side was far more serious than any of the others thus far and Lilith had needed to compensate for the shock and pain of the others in order to keep them operational.

The debris finally cleared enough to see what kind of damage they had done to the enemy. It stood in a crater with both of its front legs now missing. The bottom four arms had all been blown off and the top two had been blown in half. The top three heads were all blown apart and the one in the chest along with most of the torso armour was gone. All of the exposed skin was charred and blackened and the four MPE cores were all exposed now but the monster was already beginning to regenerate.

With only the arms on its back currently still holding weapons, now was the perfect time to attack despite the pain of their own wounds. With the broken left arm hanging uselessly at their side they picked up their borrowed weapon in their right hand and began their charge. They didn't get far when a sudden cross flare from the Angel slammed into them and sent them flying. Just as they hit the ground and began to tumble they were hit with another that sent them in different direction and slamming through the last row of derelict apartment buildings. A third hit them and sent them bouncing across the ground, ripping through concrete and asphalt and armour steel plates, coming to a slamming halt against a collapsed bulkhead for one of the lowered buildings.

In desperation Lilith was finally able to throw up their AT field to shield them before the next flare hit them. Despite the haze of pain and they could see the Angel was still regenerating its wounds while it was slamming them all over the place. The power it was utilizing was immense and unless they could come up with a way to counter it they were screwed. If they could at least do some damage to the cores and cut its power potential it would increase their chances but the way things were going it looked like they would need to do something drastic to make it happen.

Finally, some help arrived that allowed them a moments respite from the MPE's attack. The situation must have changed on the bridge because the remaining defence emplacements suddenly came to life and began to bombard the Angel. Mid and short range missiles and multi-barrelled machine guns firing pallet rifle ammo opened up on the beast, blowing off the remaining arms and tearing its back open before it could raise its AT field.

Inside the transition space the five souls operating the infamous purple destroyer were huddled closely together. In the middle was Shinji with Asuka wrapped around his left side and Rei wrapped around his right. From behind they were held in the embrace of both Lilith and Misato. All of them were shaking in pain and covered in blood representative of their wounds and the battering they had taken. Tears of sorrow and shame trickled from Lilith's eyes as she rested her head against Shinji's and spoke softly to him.

"I'm sorry Shinji," she apologized, her voice shaky. "But we need to bring out every bit of power we can and there is only one way to do that and one way for us to get there."

His eyes went wide in realization but he knew that she was right. He may not have known a lot about fighting and tactics but he knew they were in a desperate situation and this was their best chance to survive and maybe even win. She let her sorrow filled voice guide him and lead him to a part of his soul that he rarely visited but knew was there, a place where his lifetime of abuse and sorrow had filled with something that he had come to realize that he had been barely able to keep contained.

* * *

 _ **Command Bridge**_

Once the shock of the MPE Angel's transformation had run its course and Unit 01 began to attack, the bridge crew set to work now that they no longer had guns pointed at them. There would be time later to ask questions about the things they had just heard and seen but right now they needed to be professional and do their jobs. They were ready to monitor the fight and render whatever aid they could, but it wasn't going to be easy. The fighting in and out of the base had caused damage to a number of systems and they were busy trying to reroute them. They were getting telemetry from Unit 01 but they couldn't communicate with it, which was really a moot point since no one was actually still physically present in the plug to answer anyway. They also wanted to be able to operate as many of the few remaining weapons emplacements from the defence grid as they could but hadn't yet been able to get any of them to respond to commands.

Yui hadn't tried to contact Lilith through their link, partly because she didn't want to distract her and partly because she was still feeling pretty drained from using her AT field. She was grateful that Lilith taught her how, a task largely made possible by the traces of power she carried from the Second Angel. She hadn't told her about the side effects however. She felt a little like a burned out husk but she also found herself wishing that she were back in the core and taking part in this battle with her mind, her very presence joined with both Lilith and her son. She had complete faith in Lilith and Misato but she felt helpless now that she wasn't right there to protect him. It didn't help that she could tell a great deal about the ordeal they were all undergoing just by looking at the brain wave patterns on her computer screen.

A glance to her left showed her the also anxious Mari Illustrious Makinami...quite the name she had given herself...but her anxiousness was of a different variety. True, she could see concern there and unless she missed her guess the girl had become quite attached to her Shinji over the years, but much of her anxiety seemed to stem from very badly wanting to be part of the battle. She was a ball of barely contained energy, practically vibrating as she shifted about on the balls of her feet as she watched the fight, her eyes tracking every move. Her hands repeatedly clenched into fists and opened and she was clearly frustrated with having to just stand there and do nothing.

She could easily identify with that helpless feeling but otherwise she wasn't entirely sure how she felt about the girl. She knew her opinion was being coloured by the notion that if she was telling the truth she could have stopped all of this years ago and she knew that wasn't fair. She believed the girl when she said she would have if she had been allowed to, her resolve was unmistakable on that count, but it was hard not to feel somewhat upset about it though. She supposed she was being a bit of a hypocrite about it since the crux of her angst was over the way things had gone for Shinji and she was ultimately responsible for that. No amount of blame shifting even if it was subconscious was going to change that truth.

Looking to Kiel her blood began to boil at the self satisfied smile on his face. Unit 01 hadn't been able to do much against the Seventeenth yet and the battle seemed to be shifting in the enemy's favour. His smug look told her exactly what he was thinking, that he had been right about Lilith and Unit 01 not being a match for his abomination. That things were progressing towards the goal that he was seeking and that it was only a matter of time before he got there. The bastard was thinking that he had won. Obviously he wasn't believing Mari's claim that she could and would stop it if it came to that.

"I wouldn't be smiling yet Kiel," Yui said coldly.

"Why shouldn't I?" he question, still smiling. "Things are playing out right before you just as I said they would."

"Here's a little revelation that might take some of the wind out of your sails there Gramps," Mari cut in. "You know that piece of Adam that you sewed to yourself to act like a homing beacon so the Seventeenth would be drawn to it with all of that power from Third Impact? Yeah, it's pretty much useless. It's not the specimen you think it is, it's an inert sample with no active fragments of Adam's core in it."

"You are losing yet you continue to play foolish games," Kiel said darkly.

"Hardly," she sneered. "The sample you think you grafted to yourself was stolen by Kaji Ryoji and brought here to Gendo Ikari. I made sure that the sample left in its place by Kaji would pass scrutiny, which wasn't hard since only you and Holzer could access it and you never did until you needed it. You were so sure that it could never be compromised that you didn't even have it checked out closely before the surgery to attach it."

"And we destroyed the sample Kaji brought here after removing it from Gendo," Ritsuko added. "It's nothing more than a small little pile of sterile ash now."

Mari leaned in with an evil grin on her face. "So if the impossible does come to pass and your pet monster initiates Third Impact, the chances of you being rejuvenated and restore are pretty slim. A real crap shoot. If it happens, it will be more by accident than design."

"Sempai!" Maya called. "These readings for Unit 01...they're off the scale! The energy reading from its S2 organ...this can't be possible."

Yui's head swam for a moment and she had to grip edges of her console for a moment to stay upright. She didn't need to see the energy readings or the sync-graph or the brain wave readouts. She knew exactly what was happening. She turned her attention back to Kiel.

"Well Chairman," she began, her voice ice cold and a look on her face that bordered on gleefully insane. "It looks like you'll get to see just how powerful Unit 01 has become." She turned her attention back to the screen and the look on her face scared the hell out of the bridge crew. "It's the beginning of the end for the last Angel and for you."

Mari chuckled coldly, a rather disturbing anticipatory grin gracing her features. She knew what was coming and was almost vibrating in anticipation of it. In a whisper just barely audible to all present she said one word.

"Berserker."

* * *

If he were to be truthful with himself Shinji supposed that he had always been aware of this particular part of himself. The part of himself that was comprised almost entirely out of rage. The pain and loneliness he had always been aware of. Too aware maybe since it was what made him act so withdrawn and feel like he needed to apologize for every little thing. Surely those emotions were largely responsible for feeding that rage and keeping it simmering. It might be an interesting thing to find out how much of that rage was because of his father and how he had been treated for all of his life, and how much was due to his own self loathing.

He also realized now that he had been drawing closer and closer to letting that rage see the light of day ever since his mother returned to him. He was very ashamed to know that the spark for that was anger at his mother herself for her previous beliefs that had led her to leave him. He didn't want to be angry with her about that and he hated seeing her tearing herself up in blame for what she had done, he adored her and was so happy to have her back. But there was a piece of him there that felt that she deserved to be torn up about it and deserved to suffer for it. Her actions had indeed created for him his own personal little hell that he had wandered through lost and alone for the last ten years.

How could she do that to him?! He had only been four years old and she was his entire world, she was everything that he had and the source of his love and joy. As much as he had missed her he was indeed angry that she had left him. Before recent events came to pass he had never really known or understood how she had died, knowing only that when she died his misery began and he found himself angry at her for it. Had he known that she knew what would happen that day, had planned it all and had brought him to NERV to watch it, to essentially watch her die, he wasn't sure he would have been able to retain any positive feelings for her.

Every time the anger he did have toward her exiting his life rose up he would bury it deeper and deeper, ashamed of holding that emotion for someone he loved and missed so much and he thought it to be pretty irrational to feel that way. But it seemed that he could never bury it quite deep enough to forget that it was there. It was the foundation upon which all of the other things that fuelled his rage was built upon.

Plenty of extra fuel had been added to that fire of rage when he learned the truth about everything. He was angry and embarrassed with himself for having ever held out hope of reuniting with and being accepted by his father. Any man who could and would do the things that he had done didn't deserve to be thought of in such a way. While he was grateful to have met and have feelings for Rei, his own initial reactions to her truth notwithstanding, it boiled his blood to think that his father created her, conditioned her and used and abused her, specifically for the single purpose of his own sick and twisted scenario for Instrumentality.

It got worse when he gained intimate knowledge and understanding of Misato's life and how she felt. Another victim of the scenario's of SEELE and Gendo Ikari. And yes, his mother too. He loved her. Really loved her. How could he not when she had been the only person to show him any care since he lost his mother and was the only ray of sunshine in his grey and overcast little world. Even though she was consumed with the need to fight the Angels and used him to do it, she was also consumed with self loathing and guilt for that and so many other things. They both loved each other and yet they both hated themselves for it, to feel that way about someone so much younger or older, yet the feelings were undeniable. That had been made known for certain thanks to the Fifteenth and there seemed to be an undeniable connection between them.

A life filled with despair and pain had built a pool of rage that was wide and deep and all of the recent events had only expanded it and brought him closer to destroying the dam that held it all back. The way they were all synced right now had let him feel their pain and their rage as well and it felt even more concentrated and acute given his feelings for them all. Those feelings not only allowed him to empathize with them but brought out a primal, protective instinct. How _dare_ they be treated in such a way...all of them seen as tools to be used up and thrown away when their task was finished with not a care or a thought for them! All for the selfish ambitions of two men in particular.

He had never been what he considered to be strong, had never been brave and had always been too afraid to care for another person for fear that they too would leave him and tear another wound open upon his soul. But right now, with the cracks appearing in the dam restraining his rage becoming more numerous and widening and emboldening him, he didn't care about any of that. He didn't care that he was in love with a woman nearly two thirds again his age and who loved him back just as much, and he didn't care what the world would think of it. He didn't care that he was in love with Rei, a being created in a lab and who was more Angel than human and he didn't care what anyone else thought about it.

He didn't care that he had very strong and growing feelings for Asuka, despite how she had always treated him. She wasn't the same now, he could feel that the true Asuka was the one with him right now and not that phony thing that had possessed her for so long, rarely letting the other side be known. He didn't care that his affections were growing for Lilith, didn't care a damn about what she was or what anyone else would think about how he felt. Didn't care that it was something he could only describe as being primal in nature and rooted in his soul.

And he didn't even care right now that he was enraged at his mother, didn't care that she might just be able to feel the extent of that rage through the connection she had to Lilith. She should feel it. She should feel exactly what her abandonment had done to him, the scars it had left upon his heart and his soul and the true extent of the damage it had done to him. She deserved to feel responsible because she was. His father may have orchestrated much of what happened to him but she made it possible by abandoning him with a smile and a wave and a head full of foolish idealism.

All he did care about was that they all survive. He loved them and he wanted to be with them and screw anything and anybody that didn't like it. Even if to no one but himself it was about time that he admitted to his true feelings about them without all of the stammering and stuttering and feelings of guilt or the fear that he must be some kind of sick pervert. He loved them, all of them, it was a fact. He could not deny it and he would not deny it. Not anymore. He was desperate to have such feelings returned to him. He knew it yet right now in this moment he refused to feel bad about being so needy. What was wrong with wanting to be loved and accepted?

But nothing would ever come of it if they did not defeat the monster before them. This nightmare amalgamation threatened to end everything, threatened to destroy any chance they could ever have to be happy. It had hurt them and caused them pain. Caused them to bleed and to be afraid and doubt themselves and brought him, them, to the point of desperation.

The dam broke and the rage came forth, finally free. It connected with the others, connected to their own pain and rage. Lilith wept as she let it connect with her own rage and the bestial nature that she had fought so hard to shed. One last time. One last time she would let it reign because if they didn't defeat the Seventeenth then all was lost and not one of them wanted to lose the possible future.

Power unlike anything she had ever felt while part of Unit 01 surged through her as their berserker fury rose and the S2 organ taken from the Angel of Might came to full activation. The left arm straightened and healed. The deep wound on their side began to close and the smaller wounds all healed. A sudden new pain hit them as something pierced through their left shoulder. A bluish-purple spear that looked like two metal rods braided around one another was the cause.

Growling as they rose to their feet, they grasped the spear and pulled it back out. They saw another one in one of the hands of their enemy as one of the double bladed weapons it held transformed. Before it could hurl that one at them too they threw theirs, impaling their foe through the right shoulder. Picking up their faux lance they charged. With eyes blazing like the sun and roaring like a demon from the depths of Hell they were upon the Seventeenth before it could react. A swipe of their blade severed all of the arms on the left side. Another swipe stopped an attack by the arms on the right by cleaving through all of them at the elbow. They drove the blade deep into the bulky mass of flesh at the MPE's waist and left it there.

The chest mounted head snapped at them but they caught it with both hands and with a savage twist and pull they tore it off in a shower of blood and tossed it aside. Growling and snarling they sunk their fingers into the beast and tore the entry plugs out of the flesh around the cores, crushing them and discarding them like empty beer cans. The Seventeenth tried to back away from them to give itself a bit of time to heal its arms but they kept on it, clawing and tearing chunks of flesh from its body and tossing them aside, littering their battlefield with hunks of bloody meat and showers of blood.

The Seventeenth pushed the regeneration of its right arms and three fists simultaneously slammed into them and knocked them away, giving it time to throw up its AT field to protect itself. They charged right back mindless of any damage they had taken and raised their own AT field. The Angel's field showed signs of strain but wouldn't buckle. With a deafening roar they drove the fingers of both hands into the opposing field, grasped it, and tore it wide open. They lunged, this time up at the heads and mercilessly ripped and tore at them, twisting and tearing until they were gone and there was nothing but a large, bloody, gaping wound between the MPE's shoulders. They sunk their hands into the flesh and began to pull to the sides, tearing meat and snapping bone with the intent of ripping the abomination in half.

Raising up their right hand they intended to drive it down into the gaping, bloody wound, find the Angel's entry plug, and rip it from the Eva's flesh. Before they could the arms protruding from the monster's back grabbed them and hurled them away into the debris of the previously shattered buildings. Flaring their power as they rose once more, eyes ablaze and covered in the blood of their enemy, they pulverized the concrete and steel debris into little more than gravel and were about to charge again when a voice cut through the haze and penetrated their thoughts. The voice was telling them to get the Lance, repeating over and over. At first they resisted, finding the intrusion annoying and unwanted, but then they began to realize the voice was familiar. No, not just familiar, it was part of them, a part that was now separate but still connected. The voice was a large component of their anger, but it was also the reason to their brutality, the clarity of thought to their red haze of rage and destruction.

They looked across the ruined landscape to the area where the weapons building containing the Lance should have come up to the surface. The giant armoured door and the framework around it was a mangled mess that was barring the opening. They leaped over to it, leaving the Angel to regenerate behind its AT field. The voice kept urging them to get to the Lance. Grasping the edges of a chunk of twisted metal they set their feet and pulled. At first nothing happened so they dug in and pulled even harder. Metal began to move with a tortured shriek. The opening wasn't big enough yet but they could see the shattered top end of the weapons building beneath.

A warning from the voice and they instinctively put up their AT field and were knocked back by a cross flare. The field held but they were shoved back away from their goal. However, by making such an attack the Angel had done their work for them. There was now a large open crater where the damaged armoured bulkhead had been. They stalked back to the hole and reached in, pulling out the true Lance. Taller than they were the reddish purple weapon was forked like a bident at one end while the rest of it was twisted together like a braid. They could feel the power within it as they turned back to their enemy. It had picked up its five faux lances plus the one they had left stabbed into it and raised them all up in their regenerated arms. They transformed from their bladed forms into the braided spears and the Seventeenth hurled them all at once.

A sweep of the true Lance not only deflected them, but shattered them to pieces. With a furious roar they charged the Angel and using both hands they thrust the Lance forward, the pronged end twisting together as they did and rammed it through the conjoined cores in the mutated MPE's chest, shattering them. A loud, high pitched shriek was heard as the Lance tore through the MPE, a third of it's length protruding from its back with the entry plug containing the Seventeenth Angel skewered down its length and leaking LCL and blood. Like a marionette with its strings cut the MPE slumped to the ground, held up only by the Lance impaling it.

But they weren't done. They wanted to rip and tear this thing to shreds until there was nothing but pulverized, smashed pulp left of it. And they did. In moments their righteous fury had reduced the grotesque construct to hunks of bloody meat and torn up internal organs strewn across half the vacant city. Finally after much pleading the voice calmed them, assured them that they had done enough and the threat was over. The Angel was dead and they could now rest. Eventually Unit 01 dropped to one knee and bowed its head, one hand still gripping the Lance as the burning light in its eyes slowly faded away.

* * *

"NO!" Kiel screamed hoarsely as the Lance of Longinus and the rampaging Berserker put an end to his scenario. Centuries upon centuries upon centuries spent planning and plotting and formulating every detail so that he could be returned to his rightful status, all gone. A failure. He had been so close! As formidable as it was the berserk Unit 01 should not have defeated the Seventeenth. It was attacking mindlessly and should have continued to do so and been battered down and torn apart in due time.

But something had made it stop and seek out the Lance. His gaze fell upon Yui Ikari who was all but collapsed across her console. It had been her...somehow she had been able to influence the minds inside the Evangelion and direct it. It stood to reason, she a mere human had been able to manifest an AT field therefore it was not outside the realm of the possible that she was still connected somehow to Lilith. His hands tightened on the arms of his wheelchairs, arthritic knuckles popping painfully under the strain and his teeth ground together. This could not be happening! He would strangle the life out of that woman if it was the last thing this feeble old body would ever do!

"So how does it feel old man, to have everything you worked so hard for end in epic failure?" Mari asked him coldly as she stepped between him and Yui.

"You miserable bi..."

He didn't get the chance to finish as she backhanded him and sent several teeth flying from his mouth. "No one wants to hear anything you have to say," she said, her voice getting even colder if that was possible. "And I'm not a miserable bitch, I'm something you don't seem to be able to comprehend. I am a living Lance with the attributes of the Fruit of Knowledge and the Fruit of Life. Your scenario is dead and once again you have stained and shamed your race with your misdeeds. You were given a chance to redeem yourself and you chose to compound your crimes a thousandfold. You slaughtered billions and damaged this world forever, all for your selfish goals. You gambled thinking that you had all of the odds in your favour and you have lost everything. You have failed miserably and there is nothing left for you."

"Maybe not," he said, spitting out a mouthful of blood, defeat tinging his voice. "But even in defeat and seen as a criminal I will finally get to return home."

"No old man, you won't," she said. "You obviously weren't paying attention earlier so let me make this as clear as possible. I am your judge, your jury, and your executioner. Your fate was sealed the moment I made my report about what you had done here. You have crossed so far beyond any line they would tolerate that there is no going back. You have been disowned by your own kind."

She held her right arm out to her side and sparkles of purple light began to come together and coalesce into a form, the same form as the weapon Unit 01 had just used to end the Seventeenth. Kiel's mouth hung open in shock as the proof of her word about how she had been saved appeared before him. All at once the despair of his failure and the hard reality of what was about to happen to him hit him all at once. He opened his mouth to scream, to beg for his life, to plead...anything, but he never got the chance.

She thrust the Lance through his chest, its dual points protruding out through his back and the backrest of his wheelchair. "Die in despair and humiliation old man, you don't deserve anything else and no one will miss you."

His body burst into LCL and Lorenz Kiel was no more. The long nightmare he had orchestrated for the human race was finally over.

* * *

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	36. Chapter 36

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

Second to last chapter.

 **Transposed**

 _ **Chapter 36**_

 _ **Now, Unit 01's Core**_

The redhead sat by herself on the beach within the world of Unit 01's core. Her teary eyes looked out over the gentle waters before her without really seeing it and she was unable to feel the tranquility it offered. Even so, she was coping with the things she had been told a little better now than she had a couple of days ago, but she was by no means back to anything that resembled normal. That would take a while to happen.

Pretty much everything in her life up until this point was not what she had thought it was, nothing but lies, deception, and misdirection. Like everyone else she had had a role to play and hers was to be cannon fodder. She was to fight for as long as she remained able in order to keep the First and Third alive for Gendo Ikari's needs and she had certainly fallen right into that role with her superior attitude and her need to be at the forefront of every battle. Then somewhere along the way, preferably right near the end, she was to die with her death being used to help drive Shinji to such despair that he would offer no resistance as he piloted Unit 01 right into position to be the last catalyst the madman needed to realize his sick aims.

Even if she had died early in Gendo's scenario it wouldn't have really mattered. He would have seen it as a minor inconvenience and worked around it so even though he had a role for her, she wasn't all that important. It was bad enough that she had never been able to live up to her own bragging and bravado, but even if she had it wouldn't have mattered very much. When the man's own son was nothing more to him than something to be brought to ruination for his scenario, what possible worth could she have ever had other than to die on cue and help him to that end?

She had wanted the truth so badly. Well, she got it alright. She found out exactly what Rei was and why she had been created. She found out exactly how Gendo had manipulated Shinji and realized that she had been a part of his plan to keep the boy beaten down until the end. She found out about the horror that Misato had lived through and how she had been manipulated through her hatred of the Angels and her desire to destroy them to send children out to fight and she learned of the heavy toll it took on her. She learned the truth about mankind's origins and just exactly who Lorenz Kiel was and what he was trying to do and why.

She almost laughed. As strange as it sounded, the truth about the origins of humankind was probably the thing that bothered her the least out of all of it. It was the sheer madness and depravity of the rest that hit the hardest and it was her own situation that devastated her the most. By becoming so driven and allowing that other side of herself to take over and run her life she had become a usable asset. A puppet dancing on the end of a string. A doll after all.

After losing that part of herself she had already been feeling bad enough about how she had treated those around her, but after hearing the full story and now understanding the full scope of what the others had been through she felt even worse. She felt sick and was hating herself oh so very much. Just look at how she had treated Rei. The girl literally had been the Commander's obedient doll just as she had ridiculed her for being but is wasn't like she'd had any choice in the matter. Between behavioural conditioning and the use of drugs she had been made into the Commander's loyal and obedient tool. She had been stripped of even the concept of an individual identity since her soul could be moved into another cloned body if she died or if she seemed to be straying too far from her programming and thus her ultimate purpose.

She had seen Rei as just some unfeeling automaton and treated her as such but she had no idea just how much the question of her self identity plagued the girl or how painful her life was. Truthfully, she hadn't cared and wouldn't have even if she did know and saw her as just another obstacle in her way to be trampled over and she did her best to do so. But even as bad as that was it paled in comparison to the state the girl was in when she let her nearly beat her to death. She understood now what it must have meant to have the only purpose you were ever given, the only purpose you were told that mattered, and the purpose that defined your very existence taken away from you, _and then_ being left to drift without that purpose or any guidance as to what you where supposed to do now that it was gone.

Then there was Shinji. She had always berated him for his lack of commitment as a pilot, for his obvious distaste for it and not once had she ever questioned or wondered why. She had always just assumed that it was because he was a wimp and a coward. She had known that he had begun piloting with no prior experience in the seat but she hadn't thought any deeper than that. Even if she had been given more information than that she had ignored it and continued to believe that he had only become Unit 01's pilot because of his father. Well, she had been right on the surface of it but it sure as hell wasn't because of nepotism like she thought.

Her father had engaged in an affair with her mother's doctor and then married the woman, but as bad a situation as it was and as much as she had despised it, at least she hadn't essentially been thrown away and abandoned like Shinji had been. He had just lost his mother, the most loved and cherished thing in his life, and his cold, uncaring father leaves him on the platform at the train station like a piece of unclaimed baggage. When his future guardians did finally come and pick him up they treated him like an inconvenience and even while under their care he practically had to fend for himself. When his father finally summons him it is only because he has a use for him, stomping out the tiny flicker of hope the boy had that his father might want them to be a family again.

All Shinji wanted was to be wanted and he tried to do whatever he could to be seen as useful so that someone, anyone would care about him and not throw him away again. It was even a big part of why he kept piloting despite the terror he felt and the pain he endured. Despite the fact that deep down inside of herself she had felt a sameness between them and that she actually liked him, she did her level best to treat him like dirt and help keep him down just like his father wanted him to be.

She kicked him out of his own room and did her best to make him feel unwanted in his own home. He cooked and cleaned and did the laundry, essentially looking after both Misato and herself and she repaid his kindness by finding fault with everything he did and making threats. She treated him like a servant that needed to be reminded of his lowly place in life, never failing to remind him how unworthy he was, branding him as an idiot and a pervert. She took advantage of his kindness and spurned every attempt he made at even just trying to be her friend. Her disdain towards him carried out onto the field of battle, never recognizing the rashness of her own actions but chastising him for being in her way. If it hadn't been for his help she might not have even survived her first battle but she couldn't see that. Even when he saved her from the volcano she couldn't properly thank him or acknowledge what he had done.

Yet, despite every rotten thing she had said or done he had kept on trying to help, kept trying to be a friend to her and over the last few days here in the core it had been no different. Even Rei had continued to try and help her just as she had as they were making their way to the cages. Misato too, even with how badly she had treated her along with everyone else along the way. Thankfully with that other part of herself no longer present it was much easier to take that help and lean on them but it was still devastating to her to realize how little she had meant and how unimportant she had been and just how far opposed it was to everything she had ever thought or believed of herself. It was going to take a while to learn how to deal with this and get along with it. Just something else to be added to the pile she supposed.

At least with all of this other stuff she had pretty quickly gotten past the fact that they were all naked. Except when it came to Shinji. He was a boy! They shouldn't be sharing this space naked and every time she looked at him she had to jerk her eyes back up from where they kept insisting on looking. And it didn't help that the others kept teasing him and quite literally trying to get a rise out of him. Even Rei!

She closed her eyes and took a long, deep breath. She supposed that if she hadn't been taking to her therapy sessions with Doctor Tokita as well as she had been that all of this would have been even more devastating to her than it was. After needing a couple of days to even begin to digest all of this, the things she had been learning about herself in those sessions was actually starting to help her cope with this a little bit. At least that was something positive. Like Misato and Lilith had said to her, now that the threat of the Angels and everything that SEELE and Kiel and Gendo were doing was over, they could all work towards a fresh start for themselves and they could rely on each other for support. Things still felt a little bleak, but maybe didn't look quite so impossibly dim now.

"Asuka?" she heard Shinji call softly to her. She looked back over her right shoulder and immediately turned back away, her face turning red. "Baka!" she admonished lightly, not sure if it was him or herself she was talking to.

Shinji, realizing that certain parts of himself were right at her eye level as she sat there, quickly sat down beside her. "Sorry about that," he apologized. "I keep forgetting that you're not really comfortable with us being naked. Kind of weird though how I seem to have actually gotten used to it."

"You don't have to apologize," she said. "You've been in here for a lot more time than I have so..." She trailed off and they sat there quietly, neither really knowing what to say to the other. Finally she asked a question that she had been wondering on. "How were you able to handle learning about all of this stuff?"

He paused for a moment. "I don't think I really did," he answered. "It was overwhelming and I couldn't believe what my father had been doing and how he was using everyone. I think I hid behind how happy I was to have my mother back and I kind of pushed away as much as I could and tried to concentrate on that. If I did that then I didn't have to think about it and there were a lot of things happening to keep me kind of distracted but it was never too far from my mind I guess. The Fifteenth Angel...it brought all that back to the surface again. When I started to experience everything Misato had been through I thought I had lost my mind."

"Reliving your own pain and worst memories would be bad enough," she said. She didn't even want to begin to think of what would have happened to her if she had been forced to relive all of her own most painful memories and experiences again like that. She was pretty sure she would never recover from that.

"Misato and Lilith helped me get through it," he continued. "But I think I still hid a lot behind my feelings for Misato and her feelings for me just like I hid behind my feelings about my Mom. I think it was the same when I began to connect with Rei and she let me into her mindscape. Because of all of them I was feeling things I never had before and I wanted to be happy."

"Nothing wrong with wanting to be happy," she said quietly. She frowned. "As for actually _being_ happy, I'm not sure that I really know what that's like."

"I'm not really sure myself I guess," he said. "But I shouldn't be trying to use it as something to hide behind. The same goes for the feelings I have for others or that they have for me. They mean too much for me to be using them like a shield and it's not fair to the other person. I'm tired of that, I've been finding things to hide behind for all of my life so that I wouldn't have to try and deal with anything and all it did was make me miserable."

"It became rage," she said, making his eyes go wide and he turned turned so fast to look at her that it's a wonder his neck didn't snap. She didn't look up, her eyes stayed fixed on her nervously twiddling fingers in her lap. "I know it well. That other part of me...it wasn't just armour made up of arrogance and pride, it was also my rage, or at least it was like a leak in the dam that held it back. And just like you despite how much I love and miss my Momma, I would get mad too because she left me. Now I have to wonder if she was doing the same thing your Mom did or if what happened to her really was just an accident during an experiment. When that dam holding it all back finally did break I nearly killed Rei and it burned itself out. Just like yours did against the last Angel."

He took a deep breath and let it out slowly. "I feel...I don't know, I don't know how to describe it."

"Numb," she said. "Hollow. A little like a burned out shell."

He thought about that for a moment. "Yeah, I guess that is how it feels."

"It's a large part of how I've felt ever since I woke up in the hospital after what I did to Rei." She finally looked up and looked back out over the water. "I think I'm even less sure now of who I am after learning that pretty much everything in my life was based on lies and manipulation. What I thought I was and how I wanted other people to see me, that was my whole identity. Now that's all gone."

"What about being my friend Asuka?" he asked innocently. "Is that a good place to start?"

She looked over at him. "As simple as that huh?"

"Simple is good isn't it?"

She looked back to the water. "Yeah. Simple is good."

* * *

 _ **Four Days Earlier**_

If pain was nature's way of letting you know you were still alive, then Melissa Lake felt very much fucking alive at the moment, thank you very much. Before she even attempted to open her eyes she took stock of the new aches and pains she could add to the list of those she had already accumulated. For one she had a splitting headache and it felt like she had definitely broken some ribs. There was something wrong with her left shoulder, she could barely move it and her left forearm flared up in pain when she tried, it was probably broken. Her right leg was pinned it seemed and judging by the way it felt she wouldn't be surprised if it was broken too.

She slowly opened her eyes and winced as light from off to her left hit them. She blinked a few times to try and clear the blurriness from her vision with no avail, and took in her surroundings. It looked like she was in a sizable pocket in the debris and a light fixture was hanging on end by its wires, somehow still working and illuminating the space. Directly above her was her partner, looking down at her with obvious concern. He was on his knees with one hand supporting him on the floor to his right, the other was braced against a chunk of broken concrete to the left.

"Bout time you woke up," he said, relief evident in his rough voice. "I was wondering if you were going to sleep until they dug us out."

Wincing, she raised her head slightly, regretting it, and saw just how close they were. "You know cowboy, if you wanted to climb on and ride all you had to do was ask," she joked hoarsely. "You didn't have to go to all this trouble and get us this cozy little room."

"And here I was trying to impress you. I went all out and got the 'Post Apocalypse Suite' too." He choked on the last word and began coughing. She felt something wet splash across her face and neck and she realized he was coughing up blood.

"Well that's a mood killer," he rasped. "Sorry about that."

Her eyes went wide when she realized that the concrete slab that his back was pressed against was actually being held up by him. That was also when she realized that there was a piece of steel re-bar sticking out of the left side of his chest and another out of the right side of his abdomen. Blood dripped steadily from both wounds, soaking into her shirt and by the feel of it he had been bleeding quite a bit.

"Matt...!" she croaked raggedly.

"Yeah," he confirmed calmly, though the pain was reflected in his voice. "I feel like I got on the bad side of a porcupine. Those two went through and there's a few shorter ones stuck in me. I can't tell how many."

She raised her right hand and pressed it to her aching skull. Even with the light it was still dim enough that he didn't see it shaking and the majority of the cause was the two bloody pieces of steel her blurry eyes remained sighted on. "How long have we been in here?"

"Can't say for sure," he answered. "At least half an hour I think, probably more. I haven't heard any shooting for a while and the place isn't shaking periodically anymore. I think it's all over. Guess we won."

"Doesn't feel much like it," she sighed. "We're both pretty fucked up."

"Fucked up, but alive," he amended. He coughed again. He made sure not to spray her with blood this time. "But mostly fucked up," he rasped. "Fuck that hurt."

"Do you still have your radio?" she asked, feeling around her belt with her good hand but not finding hers.

"It's in pieces over by the light," he answered. "Don't know where yours is and I haven't heard any noise from it."

She began trying to look around for it but the quick movements made her head swim and throb violently. "Shit!" she swore, the pain evident in her voice.

"Don't try moving around too much," he warned. "You took a nasty shot to the head. The left side is all bloody and your eyes don't look just right. It'd be best if you just stayed still."

"Not like I can go anywhere anyway," she groaned. "My right leg is pinned. Probably busted too just like a few other parts." She looked back up at him. "So here I am mister, all laid out and at your mercy."

"And all I can do is bleed all over you," he joked back. "Talk about disappointing."

"I'll forgive you," she said. "I'll even forgive you for going all White Knight and getting yourself between me and that slab. Hard to be mad at you when you got yourself all fucked up like that for my sake."

"I know you hate that," he agreed. "Even so, I'd like to say that I saw it coming and it was on purpose but it just kind of happened this way. I'd have done it anyway even if you'd be mad at me. Alive and mad is better than dead."

"Not if it kills you instead ya big dumb bear!" she protested. "Do you know how pissed I'd be at you then?"

"As pissed as I'd be if I didn't and _you_ ended up dead," he shot back. "We're partners, we watch each others back and we take blows for each other if that's what it takes. It's what we do even if neither of us like having someone act as our shield. It's why I'm stapled to a chunk of concrete right now and despite the fact that it hurts like fucking hell, I'd do it again in a heartbeat. Besides, you have no argument to make after taking a bullet in the back a couple of years ago. Or did you think that I didn't know that the shooter was aiming for me and that you purposely stepped in between us?"

For a moment she looked stricken, as if he had given away her biggest secret. She closed her eyes, wishing she could stop the artillery barrage that seemed to be going on inside of her head. "I should have known that you knew," she said quietly. "You're infuriating that way, you know that? I'm just like you I guess, I can't stand to see my partner get hurt if I can do something to stop it. When he pointed the gun at you there was no time to do anything else so I just jumped in between. Never thought I'd do that with all the fucking noise I've made over the years about wanting to be treated as an equal in the field and not wanting to be protected." She looked into his eyes. "I can't lose you partner."

"Can't lose you either," he said, returning her gaze. "We're all each other has left. Your family turned their back on you except for your brother and Second Impact took him from you, just like it took pretty much all of my family and it cost me someone I was too young and stupid to realize meant so much to me at the time. You and me is all there is."

"Heh, I guess we're both just as fucked up as the those kids and everyone else around here," she lamented. "I lean on you more than I even know and I'm pretty sure that without you around I'd end up losing my shit. You'd probably handle it better than I would, you seem to take things in stride a lot better."

"Not so much," he answered, shaking his head. "I'd go nuts on my own, especially if you weren't leaning on me. I'd feel like I had no purpose anymore. You and I both know that being alone sucks hard and it doesn't lead you anywhere pleasant."

"No, it doesn't," she agreed softly. She was far too well acquainted with it. She winced. "Damn it, I don't think there's a part of me that doesn't hurt right now and I feel worn as fuck. We need a vacation...maybe a nice beach somewhere."

"You in a bikini, now there would be a sight," he smirked wearily.

"What's the big deal?" she huffed. "You've seen me in my lingerie before and you've seen me naked."

"First, your idea of lingerie is a sports bra and a pair of boxer shorts," he rasped. "And nearly naked does more for the imagination."

Before she could respond the piece of debris his left hand was pressing on broke off, sending him lurching towards her. A new, bloody gash was ripped into his forearm and he just barely managed to keep the bulk of his weight and that of the concrete slab off of her. Still it made her chest and ribs scream in pain and she could feel the steel rods he'd been pierced with poking into her, but by far the worst and what had her screaming was the excruciating pain in her right leg. Either the slab or something it was in contact with was grinding into the break.

With a groan of pain and effort he pushed himself back up but it didn't take all the pressure off her leg. By leaning on that piece of debris the left side of the slab had been raised a little higher than the right so it hadn't done much more than just keep her from freeing herself. Now it was grinding into her leg and he had to get it back off to both stop that pain for her and keep it from doing more damage or possible cutting off blood flow.

Steeling himself as much as he could he began to move so he could get his legs under him instead of being on his hands and knees. With nothing to brace his hands on other than the floor he had to work one leg under him at a time while attempting to push back on the slab what little he could. The pain was terrible as not just the two rods impaling him but the others that were stuck more shallowly into him moved, pulled, and twisted in his flesh. By the time he finally got his left foot under him and flat on the floor he was gasping for breath and spewing blood with every exhale. He did succeed in getting the slab raised up enough on that side that it was no longer grinding into her leg, but it felt like his back was being pulled apart.

With a lurch and a bark of pain he jerked his right leg into place so that he was now essentially in a squat. He was known for having a high pain tolerance but he had already long passed that point and it was only going to get worse. He couldn't take too much more of it and he was getting weak from blood loss. Either way it would only be a matter of time and not much of it before he collapsed on her with his two hundred and seventy five pounds and however the hell much the hunk of concrete weighed. They would both end up suffocating under the weight that was on top of them. While dying with his partner didn't sound like all that bad of a way to go, suffocating under a heavy chunk of the building wasn't quite the way he would envision it happening. He wasn't ready to die anyway and he wasn't about to let the reaper claim her either.

"Matt..." she protested weakly, knowing what he was trying to do.

He shook his head. "I wasn't...going to be able to hold it up much longer anyway." He coughed and spit away another mouthful of blood but he was still gasping to catch his breath. His left lung had been damaged by the piece of steel in his chest and it burned like it was on fire. "If...I can move it far enough...we won't have to worry about me collapsing and trapping us under it. I know it...hurts like hell...but if you can pull your leg out...do it and move as far out of the way as you can...just in case."

"Matt..." she looked into his eyes for a long moment and gave him a slight, pained smile. "You know...right?"

"Yeah, I know," he said softly with a slight smile of his own and equally returning her gaze. "You know too right?"

She nodded. "Yeah."

She noticed his right leg was shaking and saw a jagged piece of metal was sticking out of his calf. Before she could say anything he clamped his right hand down hard on his thigh above his knee to stabilize it. With a roar of both effort and pain he strained and pushed up and back, shuffling his feet to move back as he stood as high as he could. She could see the bleeding increase as the steel rods moved in his chest and abdomen. She felt the pressure against her leg disappear and using her two remaining good limbs, her left leg and right arm, she pushed, pulled, and dragged herself out of the way. She felt something snagged under her ankle and looked to see that it was her radio. It looked to be intact and the ear piece was still plugged into it but the part that went into her ear was smashed.

There was a thud and a gut tearing bellow of pain from her partner that hit her like she'd been gut shot. The chunk of concrete had slipped off of another piece of debris and tilted back, pulling the rods halfway out of him but still leaving him hung up on them. His wounds were bearing most of his weight now since his boots were barely touching the floor.

"Matt!" she rasped hoarsely, her right hand clutching the radio in a death grip.

He groaned weakly and spit out a large amount of blood as he tried to find something to get a better foothold on and get the weight off of the rods and back on his feet, but there didn't seem to be anything. He was on the verge of passing out and took the only route left to him. He kicked back at the slab and yanked himself the rest of the way off the bars. He was barely conscious when he slammed into the floor in front of her.

She found herself staring at him for a long, breathless, dead silent moment before ripping the useless headphone wire out of it's socket on the radio and calling for anyone who could hear them to come and dig them out.

* * *

 _ **Now, NERV Medical Ward**_

Her eyes slowly shifted back into focus, once again showing her the still motionless form of her partner as he lay in his hospital bed. Some guard dog she was for him, she kept either falling asleep or zoning out. Considering the shape she was in it was hardly a surprise and sheer stubbornness was probably the only reason she wasn't passed out in her own bed where everyone kept telling her she should be. At least her pig headed stubbornness had gotten her moved into the same room so she didn't have to try to navigate down the hall, trying to move a wheelchair with only one good arm and one good leg. It was hard enough as it was getting into the chair from her bed and crossing the room so she could sit by his.

Covered in cuts and massive bruises. A broken right leg. A dislocated left shoulder and a broken left arm. Six broken ribs. A hairline crack in her breastbone from the two pistol shots she took in her body armour. A broken nose and a concussion. _Everything_ hurt but she would only take just enough pain meds to take the edge off of it because she did not want to be knocked loopy or be out cold so long as he was still unconscious. She was determined to watch over him.

He was a pretty bad mess himself. The re-bar that pierced his chest had damaged his left lung and the one in his abdomen had nicked his liver. Four other pieces had pierced his back at a depth of one to three inches. One just missed his spine and another just missed his left kidney. He got lucky again with the piece of metal that pierced his right calf, it hit muscles only, no tendons, ligaments or arteries involved. The gash in his left forearm took forty stitches to close, he had five broken ribs, and like her was covered in a litany of other cuts and bruises. But he had also lost a great deal of blood. If it had taken any longer for them to be rescued he wouldn't have made it.

She kept thinking back to the things they had said while they were trapped and their enormously ambiguous confessions to one another. Here they were, both grown adults at thirty two who faced untold life and death situations every day with calmness and decisiveness, yet they couldn't articulate how they felt any better than a couple of shy teenagers. They really were just as fucked up it seemed as the pilots were, although they hadn't become overly aggressive or overly passive like Asuka and Shinji had, but in their own way they had still put up walls around themselves to prevent being hurt by losing someone close to them again. It was a natural defence mechanism it seemed to distance one's self from painful things even if that pain wasn't physical. Of course, given what they did for a living it probably wasn't a good idea to get too close anyway but it was something that they seemed to have had little control over.

They had gotten along well almost right from the start. He was a late addition to the group of recruits the Colonel had brought in, arriving about two and a half weeks into their 'boot camp' process. While the SIS itself was about as free of sexism as you could get, the group of recruits weren't quite so enlightened and those first couple of weeks had been pretty trying for her. She could handle it and while she tried her best not to have busting someone's face be her first response, it didn't always happen that way and every scrap only made it worse.

By the time Matt arrived she had gotten a little bit bitter...well _more_ bitter and was just waiting for more of the same shit to come from him. Turns out they were closer to being in the same boat than she had thought. While she caught shit from the others for being a woman and a damn good looking one at that, he caught it for his size. At six foot eight and two hundred and seventy pounds the others saw him as a challenge to be met, that just because he was big he must think he was superior and needed to be brought down a notch, especially since he was late to the party.

She learned early on in training that he was nothing like the others. They got paired together for hand to hand sparring and he didn't pull any punches or treat her any differently than he did any of the others. He hit hard and it was her challenge to keep from being hit and she loved the fact that he wasn't afraid to knock her out if that's what it would take and he made no apologies. He expected her to be good enough to handle it.

They were also paired together for group exercises and while he wasn't the most talkative person at the time, they worked well together and he never once said or did anything that showed any animosity or resentment towards her. Not even when it was her turn to lead the pair during drills. He trusted her judgment and followed her lead, just as she did when it was his turn. The clincher for her overall opinion of him though was when one of the more bothersome louts got a little too full of himself one night and was bragging at the bar about how he was finally going to put her in her place.

When Matt slapped one of his big paws down on the guy's shoulder she was just about to tell him to piss off and that she didn't need his help to take down the jerkwad. She was surprised though when Matt told the guy, loud enough for everyone to hear, _"If you think your balls are big enough to take her down then shut your fucking mouth and go do it...just don't come back crying when she uses your ugly fucking face for a floor mop."_

The guy was more of an instigator than a doer, but Matt had put his back to the wall with his buddies so he had to either put up or shut up. The look that Matt gave her as he shoved the guy in her direction told her everything she needed to know. That look said _'Kick his ass, I've got your back.'`_ Kick his ass she did and it wasn't even close. Together then they proceeded to kick the asses of all of his buddies when they decided to get involved too and were sitting together at the bar having a beer when the security personnel finally arrived.

Early the next morning all of them were lined up in the main 'classroom' of the camp and being faced down by a very angry Colonel McKinnley. They were read the riot act and informed of how in all of his years in both the SAS and in running the SIS he had never seen such a collection of disgraceful idiots. Many of them were surprised that what they thought was loose supervision by the training camp staff was actually part of the entire exercise to see how they all interacted without interference from their overseers. The Colonel didn't just want top flight field operatives, he wanted good people with integrity and character. They were informed that the camp was coming to a premature end because of their actions and every single one of them had to stand before the group and listen to the Colonel's assessment of them and he didn't pull any punches. They were the last two he got to and they were the only ones who weren't booted from the camp in disgrace, being exactly the kind of operators he was looking for.

The others were mortified and got a bigger shock when they found out that of the twenty in the camp, her and Matt were the only ones who had been recruited to attend and hadn't gone through an application process. Even worse, the Colonel informed them that a full report on every one of them would be going back to the Commanding Officer of their regular units along with them and that their conduct here would be part of their permanent service record.

After the other eighteen were escorted from the room to be processed out, the Colonel just stood and stared at them for a long while as they stood at attention before him. After several minutes he cracked a smile then began to laugh. As a reward for exceeding even his expectations for them they got to spend the next two weeks with him recruiting new hopefuls for the SIS, no more applying for it and then wasting time weeding out garbage like the last bunch. He would get recommendations from his network of trusted contacts and the three of them would go scout the talent. After all, they needed a new class of recruits to test themselves against before the real training started.

Once they started taking field missions they quickly became the best the SIS had. They worked together so well that it was almost uncanny, as if they had trained together their whole lives. Out of the field they became pretty much inseparable and the best of friends, and there was never any question that whatever they decided to do with their downtime most of it was going to be spent together. They really were all that each other had and life seemed to be much easier to navigate together. With the SIS and him specifically, she had finally found someplace where she fit.

Even with as well as they got along it took a long time before they began to open up about the more personal aspects of their lives and started to get to know each other as well as they did now. It had actually been good to be able to share that with someone who knew where she was coming from, who understood about losing someone close. It made her feel less alone somehow. She didn't know exactly when their unstated connection to each other became what it apparently was now, that was how seamlessly it had happened she guessed. Without even knowing or realizing it they became silently and irrefutably intertwined. It was nice and kind of frightening all at the same time.

The truth was, they needed each other. They were the best at what they did because they had the skills to do it, the resolve to do it, and they were cold enough to do it, but they did their best not to lose their humanity and that was one of the most important things that they did for each other. Their job was not one that you could do without retaining some shred of your humanity or else you were in danger of becoming what you hunted. It was also not a job you could do without taking a break now and then and they had been at it for too long of a stretch the last couple of years. Their desire to hunt down SEELE was pretty much an all consuming crusade and they had been in almost constant action since she went active again after getting shot. They had been walking that razor sharp, jagged edge for a little too long now without respite and she could feel her sore, aching body, and her current ragged and worn mental state perfectly reflecting how she felt inside right now.

After coming to Tokyo 3 and learning about the people here that they became involved with, she was kind of amused to see the parallels between her and Matt and Shinji and Misato Katsuragi. Matt kept his personal apartment relatively neat while she was a slob and her place usually only got cleaned if he came by and then gave her the gears over it before helping her tidy up. He could cook while she relied on take out and anything she could toss in the microwave. He could play an instrument, the guitar and he was good at it, while she didn't seem to have an artistic bone in her body.

On a more troubling note, when she also emulated Katsuragi by getting drunk off her ass to chase away a demon or two, Matt was always there to take care of her, even if he had been drinking with her so that she didn't drink alone. She really hoped that Katsuragi came out of the Evangelion okay so that they could renew acquaintances. She could finally introduce her to Matt and no doubt she would tease the hell out of her over him. When they had spent time together when she was in Germany she hadn't realized just how much she talked about her partner until Misato had started teasing her about him.

But, she would have to get out of the Evangelion's core first and Matt would have to wake up and she didn't know if either one of those was a sure bet. She'd give just about anything right now to hear him give her the gears about something, or make one of his horrible puns, or tease her about being a nasty bitch that no one liked. It was bullshit and he knew it but he only did it because she tended to scowl more than she smiled and coupled with how tall she was some people tended to think she was even more of a hard ass than what she was. It was kind of the inside joke of the SIS, like she was their boogeyman or something.

"Wake up already Canuckle-head," she pleaded softly. "You've been asleep for four days, that's long enough don't you think?"

"Oh no, what has happened to my Big Bear?" a worried sounding, German accented, female voice suddenly was heard to say.

She turned quickly in that direction, a movement that her wounded head was not at all in agreement with, and was greeted by the sight of a short blonde haired woman wearing desert sand coloured shorts and a matching short sleeved uniform shirt worn open over a black tank top, and a pair of worn hiking boots. It was quite a surprise to see their friend Mina Krause of GSG-9 standing just inside the door. She had been so preoccupied with her thoughts and worries that she hadn't even heard the door click open.

"Mina...what are you doing here?" she asked.

The German woman walked up to the end of the bed, her concerned eyes never leaving its occupant. "I think the Chancellor had an attack of guilt for not letting us be part of the hunt for SEELE or for allowing us to come and back you up here before now. She is embarrassed that so much of the shit was coming from our country, especially Kiel and the mercenaries." She looked over at her. "The Colonel gave me and Ehrlich the full briefing, I know what you know. I suspect I got just as drunk afterwards too."

"Even he got totally shitfaced," Lake said. "First time I ever saw him _that_ drunk. He actually passed out."

Mina's eyes went wide. "That's a lot of booze, he's like a fucking camel. He out drank Vogel that night in Munich and that's not supposed to be possible. _And_ he walked back to the hotel."

"More like stumbled but that might be because he was carrying my immobile and incoherent carcass on his back," Lake admitted. She closed her eyes and winced, rubbing her head with her good right hand.

"You okay Cowgirl?" The blonde asked. "And don't say you're fine. We talked to the doctors and the Colonel so I know how wrecked you are."

"The headaches from this concussion are a bitch," she sighed. "Could be worse though, at least it just scrambled my brains, the doctor said if I got hit any harder it likely would have busted my skull. Gonna take a while before I'm right again. As fucked up as I am though, at least I'm awake, even if they think I should be spending my time asleep instead of sitting here."

The German sat on the corner of the bed. "You should be but I know you won't, just like he wouldn't when you got shot. Funny how when the _'Hands of the Reaper'_ end up in the hospital it's always together."

"People still call us that?" Mel smirked.

"Among other things," Mina chuckled. "There are a lot of groups of bad guys out there that want you two dead but they're too scared of you to attempt it. They just hope they can skate along doing what they do without you noticing. Over the last couple of years especially the two of you have built a fearsome reputation." She gave the taller woman a look of false anger. "One of the last groups we took down were actually relieved that it was us and not you and the Big Bear that got them. Talk about humiliating."

"I'm sure you got over it Monkey Girl," she drawled. "Probably went and climbed up the side of a building or something to vent your frustrations."

"It was the President of Deutsche Bank's condo building actually and I got pictures of him knocking boots with a suspected agent of the Chinese government." She sighed. "Even when I try to play, work intrudes."

"I'm sure you'd have rather climbed him," Mel said, jerking a thumb towards her partner.

"Been there, done that, and _really_ want to do it again," the blonde admitted proudly with a big, happy grin. "I take it you still haven't?" She smirked when the tough as nails Cowgirl gave her the finger but otherwise avoided her gaze. It was the closest equivalent to a blush anyone would ever get out of the hard ass, though she would never ever admit to it and poking her about it would literally be fighting words. When her friend still hadn't responded she took another dig.

"I'm not greedy, I'll even share him with you. Hell, I'll even help you out. I'm not against going both ways, especially if it's the two of you."

"You sure you didn't fall on your fucking head after you climbed that condo?" Sadly, if there was one thing that she had never put much thought into it was her sex life or the general lack thereof. She couldn't say though that she didn't find Matt attractive, but most of their time together had been spent taking bad guys apart and keeping themselves from falling apart when they weren't. As stupid as it sounded it was almost like they were too close to get close _that_ way. And now Mina...fuck she didn't know whether to take her seriously or not or how she should feel about it if she was freaking serious. Right now, she was way too fucked up to even worry about it.

"So he was playing hero was he?" Mina asked, giving her a break.

"He claims it was coincidental," she answered, glad for the reprieve. "Idiot said he would have done it anyway even if it wasn't." She looked over at him, her eyes taking on a distant look. "I woke up to see him over me holding up a fucking slab of concrete and with two pieces of steel run through him. He was bleeding all over me and I could see how bad it hurt but he acted like it was no big deal."

"Just like him," Mina agreed. "Are all Canadians like him?"

"Couldn't say," she answered. "He's the only one I know." She turned to the blond. "What am I going to do if he doesn't wake up? He keeps me sane and human. He's that big fucking immovable object that's always at my back."

"Good thing...you won't have...to find out," he told them, his voice weak and groggy. They were greeted by the sight of his green eyes slowly cracking open. "I'm not...that easy to...get rid of...remember?"

"You big, stubborn...don't fucking scare me like that," Mel admonished quietly.

To Mina's ears it sounded like she was trying very hard not to let her voice crack with too much emotion. With a mischievous grin on her face she got off the corner of the bed and stepped around to Mel's right, took her hand and placed it over Matt's. Not coincidentally she left her hand on top of both, mostly to make sure they stayed like that but also to let her friends know she was there for them both.

"Don't be such a wimp Cowgirl," she admonished lightly. "Or are you too afraid that someone might see you being something other than hard as a rock? Truth is I'm ready to cry too. Stupid pride...we're all fucking idiots."

"Sorry," he apologized thickly as he wiggled his fingers a little to let both of them know that he appreciated the gesture.

"I knew you wouldn't die but you scared me too Big Bear," Mina said. "When you get better I expect to be compensated for that. We both do, even if she won't admit it." Mel tried to glare at her but it lacked fire and she cheekily just stuck her tongue out at the brunette in response.

"Don't get ahead of yourself Monkey."

"Half dead and I still have two women fighting over me," he said, sounding a little bit more coherent. "I must really be something."

"Want me to tell you what?" Mel cracked.

"Don't worry Matty," Mina said. "I'll keep the evil bitch at bay and nurse you back to health."

"I can just imagine what that would entail," Mel snarked lightly.

"I'll go tell the doctor that you finally woke up," Mina said, giving her the finger. "Try not to jump him while I'm gone Cowgirl."

"It took me ten minutes to get myself into this wheelchair and it will take twice that to get back out," Mel shot back. "I'm pretty sure he's safe."

The German just smirked at her as she walked out of the room, adding a little extra wiggle for his benefit.

"Crazy as a fucking bed bug," Mel huffed. "No wonder we like her."

"She's our kind of crazy," he said thickly. He gave her a wink and squeezed her hand. "You're a mess, but thanks for being here."

"And you're not?" she said, squeezing back. "Where the hell else would I be?"

* * *

Please leave a review if you would be so kind.

And while you're here, check out my other stories.

Someone will probably bitch about this chapter but I really don't care. Like with everything I write, I write what _I_ like.


	37. Chapter 37

**Disclaimer:** I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

Last chapter.

 **Transposed**

 _ **Chapter 37**_

 _ **Auxiliary Cage Control Room**_

With the damage done to its usual assigned cage, upon recovery Unit 01 had been moved to the auxiliary cages where it was being closely monitored. It was the morning of the fourth day after its triumph over the last Angel and the pilots had yet to return from the core. Yui had been in brief contact with Lilith to check on everyone the previous day, she had been down herself for a couple of days after the strain of using her AT field and being in telepathic contact with the berserk Evangelion. Being in contact meant that she had been exposed to the rage and in particular the rage and anger of her son.

In a way she was actually glad that he was angry with her. He should be and she deserved it, she deserved every bit of vitriol he felt towards her and she deserved to feel all the same pain and heartache that he felt. She thought that she knew how much she had hurt him but what she felt during that contact showed her that she knew nothing at all. What could she possibly do to ever heal that deep hurt? How could she even begin to make amends?

Despite the couple of days away she still looked a little worn but refused to be away from things any longer. Apparently the pilots were recovering from their ordeal but the hold up in their return was largely due to wanting to make sure Asuka was alright after being told what had really been going on. She could only imagine how hard that had hit the girl. They had all been in rough shape right after the battle and Shinji had been exhausted but Asuka had the added burden of her world being turned inside out for a second time.

Ritsuko was viewing plug data from the battle while waiting for results from diagnostic checks on the MAGI, as well as keeping an eye on the scans and readings from Unit 01. She was fascinated by the plug data and was chomping at the bit to be able to find the time to really get into it and study it. Beside her, Ibuki was coordinating with the rest of the crew on the main bridge as some of the higher priority systems that had been damaged were being repaired and brought back on line. Personnel were being brought back to the base as needed to make repairs and run vital systems while engineers were checking the access points above ground and having buildings raised back into place as they cleared each plot. Except for the area where the battle against the last Angel took place, there had been little damage done to other parts of the city.

Fuyutsuki stood by the observation windows, a cup of coffee in hand as he regarded the the still form of Unit 01. Having just arrived Yui was sitting at a console next to him taking a look at the readings from the unit herself. Nearby was her new shadow, Mari. After disappearing for several hours after the battle to make her report to her mentor, she had returned and taken up the role of bodyguard for his former student. It was believed that all of the invading mercenaries had either been killed, captured, or had managed to escape but Mari wasn't about to leave Shinji's mother unattended. She had visited the places where she knew the mercenaries had been holed up before the attack and cleared them all, picking off a couple of stragglers as she did. He had little doubt that she had also hunted down any she had tracked outside the base as well.

"Are you sure you're up to being here?" he asked Yui.

She smiled at her old professor. "I'm fine. I used to be in worse shape than this at times while I was building the Evangelion."

"That's true enough," he agreed. He wasn't buying it, he could see that something was weighing on her but this wasn't the place or time to address it. "Have you had anymore contact with Lilith?"

She shook her head. "She'll contact me if there's a problem or when they're ready to return."

"I don't think it will be too much longer," Mari spoke up, causing them to look her way. "I can feel people's souls, even theirs while they're in the core and they all feel like they're doing okay, no serious levels of distress. Even Asuka seems to be doing better, it feels like she's calmer. I think someone's teasing Shinji though. He feels a little flustered."

"Misato," Ritsuko and Yui both said at the same time, eliciting a laugh from everyone.

"I have the ability to go in there and bring them out if needed," she reminded them.

"I think you're just impatient to introduce yourself to Shinji-kun," Maya cut in. It was uncharacteristic for her to butt in and with a joke of all things and that was reflected in the reddening of her face. But since getting closer to Ritsuko and having been so deeply involved as of late she was feeling a touch bolder, more sure of herself and her place.

"Guess I can't deny that," the alien girl said happily, suddenly changing her attire from her school uniform to her pink plug suit, which wasn't quite fully zipped up.

"Down girl," Yui said, reaching over and zipping the suit up. "Don't want to give him a nose bleed right off the bat do you?"

"No fair being built like that at her age," Maya grumbled, thinking no one heard her.

"You're fine as you are Maya," Ritsuko said through a smirk without looking up from her screen.

"I'm actually a few hundred years old Maya-chan," Mari laughed. "But I'll take that as a compliment." She sighed. "I just hope Shinji...and the others don't hate me for what I did. Or didn't do I suppose."

"While I can't really speak for the others I'm pretty sure they won't hate you," Yui assured her. "It might be a shock to them but I think they'll understand, especially now that they will know about the First."

"I hope so," the girl said, her true concerns finally bubbling up through her otherwise cheerful demeanour. "I want to have somewhere I can belong, where I can have friends and live a real life. I really hope it's here."

"I think you'll get your wish," Fuyutsuki said. "Despite all of the things they have had to endure I have seen some positive things in those children, especially most recently. Even if it's not immediate, I think everything will be fine."

"I don't think you'll have too much trouble with Misato either," Ritsuko chimed in, finally looking up. "She may have some anger at first considering the her hatred of the Angels and having to send the Children out to fight, but if anyone understands the ugly side of following orders or doing what's necessary...and despising herself for doing it, it's her. She'll understand your situation and she's not such a hypocrite that she'd hold it against you. I just hope she can do the same with me. The things I was doing and the secrets I kept put a hell of a strain on our friendship."

The door to the control room opened to admit Colonel McKinnley and Kaji, with the Colonel looking a little worn himself. Things had been hectic for him as he oversaw the mop up of the battle against the mercenaries as well as the aftermath where he had to deal with the Japanese government and military as well as the UN. He also had several investigations on the go to keep track of but he also had to deal with the loss of some of his personnel and having his two best operators wounded and in the hospital. It was clear to them all that he cared a great deal for his people and those two in particular.

He sat down heavily at an open console and leaned back in the chair for a moment, closing his eyes. Kaji went to the coffee maker they had set up in a corner and drew a mug for both himself and the Colonel. It was odd and almost a bit comical how the former triple agent had seemed to become a constant at the older man's side.

"Are you alright Colonel?" Yui asked.

He took a sip of steaming black brew. "A cup or two of this and I'll be right as rain," he said. "Just so long as I don't have to sit through anymore meetings with politicians. They are the last to get anything and the first to act like they were never issued a brain. And it doesn't matter what country you're in, they all seem to be exactly the same."

"The meeting with the Prime Minister didn't go so well I take it?" Fuyutsuki asked, taking a seat himself. He could identify, he had met with plenty of government officials in his time as Gendo's second.

"It went fine after it was made clear to them that they weren't in charge," Kaji answered.

"A couple of the Prime Minister's cabinet members wanted to try and play the 'this is our country therefore we have jurisdiction' game with us," McKinnley explained. "They needed to be reminded that this and _all_ of NERV's facilities fall under the control of the UN, something that they and every country that has facilities agreed to and signed off on a long time ago."

"Their fall back position was that such agreements should be torn up because the UN had been heavily infiltrated and compromised by SEELE loyalists," Kaji continued. "That ended when they were reminded that one of their very influential and close friends was a member of SEELE's ruling committee and was influencing the Home Affairs Minister. Also that one of their elite JSSDF units was under house arrest for being part of the plan to attack us, _and_ one of their regular force units did turn their guns on us when the attack started."

"When the Secretary General hinted that a tribunal may well be set up at the conclusion of a number of ongoing investigations and that the Prime Minister was giving his full cooperation they started singing a different tune," McKinnley said. "It seems that these two particular ministers may have been involved in some way. Be it inadvertent or deliberate, that is yet to be determined."

"So what will happen going forward?" Fuyutsuki asked.

"Personnel at all NERV facilities will be interviewed to determine who knew what in regards to the true aims of both SEELE and Gendo Ikari," McKinnley answered. "As it pertains to this facility in particular, since I'm already here I'll be overseeing it and two of my best investigators and a forensic psychologist should be arriving within a couple of days to get started. It also means that you all will still be under watch and accompanied by my personnel wherever you go. Personally I have no worries that any of you are up to anything or are about to try and leave but this is a protocol that has to be followed given the circumstances."

"Considering what went on here it stands to reason," Ritsuko said sombrely. "I guess I should consider myself lucky I'm not in a jail cell."

"There were some that were pushing to have everyone with any sort of a position of authority at all locked up and the key thrown away, but most of those people will be under investigation themselves," the Colonel said. "I convinced the Secretary General to let me handle it since I've heard enough of your stories to know what happened here and a lot of the how and why. With that said I must urge and caution you to be absolutely truthful with the investigators about everything because it can make the difference between remaining free or not."

"Absolutely everything huh?" Ritsuko mused. She really didn't want to recount to anyone how she came to be ensnared in Gendo's web, that had been hard enough to talk about with Yui and Maya.

"I've already been interviewed by the people that are coming," Kaji said. "There's no need to worry. They are very thorough and very professional. They are aware of how Gendo did business."

"Will they be interviewing the pilots as well?" Yui asked.

"I'm afraid so," McKinnley answered, his tone apologetic. "I know that they have been through more than enough already, but it is necessary. Ricardo and Robert are the best at what they do. They can break the most hardened criminal or gently get information from a traumatized victim with equal skill. The pilots will be in good hands."

"What's going to happen to NERV after this?" Maya asked.

"There are more discussions to be had but the Secretary General would like it to go back to being a research organization," the Colonel explained. "And he'd like the existing personnel to remain to help staff it. Since I'm familiar with the situation here, at least for a while my team will remain to provide security and oversight, and to be honest keep tabs on those who were part of Gendo's plan as well. I'm afraid that has to be part of it."

"Not surprising really," Fuyutsuki sighed. "I will consider myself fortunate if being watched is the harshest punishment I face. I suspect however that my conscience will punish me more than enough as it is."

"I believe that was taken into consideration after Kaji and myself expressed our observations to the Secretary General," McKinnley continued. "And you should know that the involvement of people like yourself and Doctor Akagi will not become public knowledge. Within a few weeks the UN will be releasing as much of the truth as can safely be told. The secret society known as SEELE is the villain who sought to destroy mankind in its misguided aims to force mankind's evolution. The story that Kiel sold to the rest of the Instrumentality Committee will serve well as the focus for this because it can be backed up by surviving members. They had no knowledge of his true aim.

Kiel's and mankind's true origins will not be revealed, nor will the machinations of Gendo Ikari. That should serve to keep NERV personnel here from being unjustly vilified by an angry public and cut down on some of the expected security issues. We want all of the focus to be on SEELE, but there will still be believers in that cause and Angelic cults running around, not to mention the usual criminal parasites who will move in and try to take advantage as this city rebuilds and gets back on it as feet. That's part of the reason why my personnel will remain here and I plan on putting Lake and Riker in charge of weeding out the whackos and crooks once they're healthy enough again. They've been constantly on the go for a long time chasing SEELE all over the world, it would do them good to stay in one place for a while."

"Speaking of those two, how are they doing?" Yui asked.

The Colonel's entire posture seemed to sag a little, again an indication of how much he cared about the pair. "Matt is still unconscious and they had to move Mel into his room since she wouldn't stay in hers. Even with that measure she won't stay in bed where she should be, she insists on sitting next to him and waiting for him to wake up. At least they got her to use a wheelchair."

"One of the doctors threatened to sedate her so she'd stay in bed and she threatened to sedate him with her fist if he tried," Kaji spoke up. "Even all banged up like that she's _still_ scary."

"She's in protection mode because her partner can't defend himself right now," McKinnley said. "He was the same way a couple of years ago after she had been shot and was out for a couple of days, despite the fact that he had been wounded as well." He sighed. "Seems like the only time I can get those two out of the field for any length of time is when they're stuck in a hospital."

"They certainly have our thanks for protecting the children," Fuyutsuki said sincerely. "As unconscionable as it is for us to need them to pilot the Evangelions, to be willing to hunt them down and kill them, for money no less, is beyond depraved."

"And the men hired to do it were some of the worst in the mercenary world," McKinnley added. "At least now they will no longer be a problem for anyone." He smirked. "And on a related note it seems that the German Chancellor had a severe attack of conscience after she was given the sanitized briefing on Kiel and SEELE. She swallowed Kiel's cover as a wealthy if reclusive philanthropist and was manipulated into a few situations that ended up benefiting him. It seems she had also done like a couple of her predecessors had in hiring mercenaries through the Bittrich Foundation to do off the books black ops that she didn't want to be seen as government sanctioned if they were found out about."

"In an attempt to brighten her image and ease her conscience she has loaned a team from GSG-9 to work with the SIS here," Kaji continued.

"Too bad she hadn't had this attack of conscience before hand," the Colonel groused. "We could have used the help during the attack and this particular team has worked with Lake and Riker before and they've worked well together."

"What about the Evangelions?" Fuyutsuki asked. "Now that the war against the Angels is done there are those who will either want them for themselves or be making demands about their status. I hate to bring a dark shadow back over us but we have been aware for some time that certain parties would not be against taking them by force."

"The Secretary General has already had that hot potato land in his lap," McKinnley said. "Since NERV is part of the UN, the Evangelions essentially belong to the UN. However the biggest trump card he holds is the fact the there isn't a single government in the world that has raised this issue that didn't have people in very high positions tied directly to SEELE and he has the evidence to back it up. Because of this if they continue to make too much noise over it they make themselves look like SEELE loyalists trying to further their agenda."

"They are already going to be under heavy scrutiny due to the individuals linked to SEELE," Kaji continued. "They don't want their entire government to be seen as having participated in a potential end of the world scheme. Even they know that's not a situation they can shrug off or sweep under the carpet. There isn't a closet big enough for them to hide that skeleton in."

"UN Military units and intelligence assets are already being deployed to guard against any potential hostile intents," McKinnley said. "Both publicly and through diplomatic channels it is being made known that any action taken against this facility, its personnel, or any attempt that is made to damage or obtain the Evangelions will be met with extreme prejudice. We fought a hostile outside invader, we don't need any human based conflicts to pick up where that left off. We lost half the population at Second Impact and millions more in the wars that followed. Sadly money seems to mean more to them than lives and the toll this all took on the world economies alone should make them unwilling to spend more blood and treasure. The fight took place here, but the world is weary from the fight and people won't stand for more. Hopefully the politicians will have had enough as well."

At that moment his phone buzzed with an incoming message. He dug the device out of his jacket and read the text. He let out a relieved sigh as he lowered the phone, leaning back and closing his eyes for a moment."

"Colonel?" Yui questioned.

"A little good news," he said as he sat back up. "That was from one of the officers from GSG-9 that went down to the hospital for a visit. Matt just woke up."

"More good news, they're coming back!" Mari exclaimed a mere second before an alarm at Ritsuko's console warned her of activity in Unit 01's core.

Yui felt a hand come down on her shoulder just before her world blurred and shifted and she found herself standing in front of Unit 01. Disoriented, she nearly fell down but Mari easily held her up.

"A little warning next time maybe Mari-chan?" she suggested to the alien girl.

"Sorry," the girl smiled cheekily. "But it was the fastest way to get here."

The core began to glow and with a loud, wet squelching sound a mass of, naked, intertwined flesh landed before them with a splash. Shinji was on the bottom with Misato clinging to his right side and Rei to his left. Laying face down on top of him was Asuka and holding the whole group together with her arms wrapped around them as best as she could manage was the dark skinned form Lilith. All were unconscious except for Lilith, who proved to be only just barely awake as she rolled off and onto her back, staring up at the ceiling.

"That...was a lot harder than I thought it would be," she said with a tired sigh.

Yui knelt down next to her long time friend and partner, ignoring the LCL soaking her legs. "Welcome to the outside world," she said. "Thanks to you and them it's still here for you to discover and explore."

"You were part of that too," Lilith said. "If you hadn't spoken to us and calmed us we would have lost ourselves." She looked over Yui's shoulder at Mari, instantly sensing that there was something both different and familiar about the girl. "So who is this?" she asked guardedly.

"That's going to take a little explaining," Yui answered. "But she is indeed a friend."

Mari however wasn't paying much attention to them as she stood looking down at Shinji and the others with her hands resting on her plug suited hips. She was pouting slightly.

"No fair. I am so jealous right now."

* * *

 _ **Five Weeks Later, The Aurora Restaurant, 45 Floors Above Tokyo 3**_

For the first time since the end of the conflict versus the Angels, the atmosphere felt relieved if not totally relaxed. There were still a number of investigations going on but the in depth interviews had all been conducted, everyone's role in things had been defined, and their fate going forward decided. The world at large had begun to be told of the boogeyman that had been in their midst that was SEELE and what they had been responsible for. Predictably the response had been ugly and there had been riots and violence but for the most part the entire situation had been steered in the direction orchestrated by the UN Secretary General, Colonel McKinnley, and a small number of others who could be trusted to spin the story even if they hadn't been told everything. There would be rough spots for a while but they were confident that things would be kept from getting out of control.

But politics and the fallout from Kiel's scenario were the least of the concerns on anyone's mind this night. While there would be more celebrations to mark the end of the Angel War this one was a more limited event. For both the aspects of ease of security and a desire to splurge a little, the best restaurant in Tokyo 3 had been rented out for the night. The guests were the senior staff of NERV and the SIS, the pilots, and the defenders of the base from that final battle that were able to attend. While the Secretary General of the UN had been invited his duties had kept him away, though he would be making an official visit sometime within the next month. In his stead he sent one of his senior aide's to convey his gratitude and well wishes to all present.

It was a relatively formal affair but not strictly so. Still, for most it was nice to dress up a bit and eat, drink, and make merry with their comrades and the new friends they had made during the turmoil. One of the most interested observers of it all was Lilith as she stood by the panoramic windows that surrounded the top floor restaurant, on the side looking out over the downtown core of the rebuilding fortress city. She was dressed somewhat grudgingly and uncomfortably in a simple white blouse and dark skirt. Even light and loose clothing felt horribly unnatural and restricting to her and she often refused to wear anything while at home in the temporary apartment shared by herself, Yui, and Shinji. It was amusing how Shinji was almost perpetually blushing because of it and how Yui was slightly put out by it since she had to cover up for Shinji's benefit. She may have a nice body but poor Shinji didn't want or need to see his mother naked and she made sure to tease Yui about it whenever she could.

A quick and temporary renovation had adjoined their apartment to the one next to where Misato, Rei, and Asuka were staying. Rei seemed to have no hesitations about wandering around naked and at times neither did Misato. At least half the time when she was clothed she might just as well have been naked anyway. As for Asuka she kept protesting their actions, reminding them with a face as red as her hair that while the state of being in the Evangelions core world may have been nudity, they were _not_ in the core now. Her protests may have been a good part of the reason why Rei and Misato paraded around naked as much as they did. The other reason of course being Shinji. Poor boy, he and his burgeoning teen hormones just could not catch a break.

It also didn't help him that on their transition out of the core she had de-aged Misato a little as repayment for having yanked her into the core in the first place. One of the great things about having your body reformed when you came out of the core was that it was essentially a new body with no mileage on it. You couldn't change what you looked like since that was defined by your soul, but you could peel back the years. She and Misato had discussed it and as much as she would have liked to be a teenager again, Misato would have still carried the same adult memories and mindset despite her own admitted level of immaturity at times and would have felt far too much like what she would have been, and adult in a child's body.

There was also the headache it would cause with the outside world as to how she got that way which would end up in revealing who Lilith really was and that was not knowledge that the rest of the world needed or would be able to handle. So they decided that when the time came they would compromise and shave a few years off. She taught Misato how to visualize the way she wanted to be. She wouldn't be able to help too much with it since she would be concentrating on getting them all out of the core intact. In her excitement Misato almost went to far and had to scramble to fix it before the emerged and came out looking more like a twenty year old than a near thirty year old. A young twenty at that. It was a bit of a screw up but they could work out an explanation to cover it far easier than if she had came out looking fifteen.

While she may have been the entity that gave rise to the human race, Lilith had never had the opportunity to truly observe them and she was finding it to be a fascinating thing to do, especially up against her knowledge of the highly advanced race she came from. While she could read thoughts and minds if she so chose, it was not the same as being able to watch the people and learn about them just through simple observation.

The way the people came back to this city in the aftermath of the war was nothing short of amazing to her. They had built the city, they had built lives here and it was in mankind's territorial nature to not want to give up what they invested sweat and blood into. The majority of those who had left came back and began to rebuild anew and those that had never left took a leading role. There was a smattering of discontent between the groups with those that had risked everything to stay here being critical of the views and ideas for reconstruction coming from those who they felt couldn't abandon the city fast enough during the conflict. It was a not unexpected problem and there were people willing to mediate a compromise to keep the peace.

Her observations however also served to remind her of something she hadn't really taken into consideration while she was still in the core. She knew virtually nothing about the modern world or how to live in it and she was totally dependant on Yui, Misato, and the children to help her navigate through what had turned out to be a totally alien existence to her. Just the sensory experiences of the world alone were almost too much at times, far more acute and defined than her senses in the Evangelion had let her feel. For a very long time as she was in her semi slumber, she could sense her creations all around her and feel things from them but it wasn't the same as her own reactions and experiences, Even after she became 'awake' inside the core her only real experiences came from Yui and from synchronizing with whoever sat in the pilot's chair. Feeling and experiencing things first hand on her own now was a long forgotten and very different thing.

There was also the trust factor that weighed upon her. While few knew just exactly who and what she was, there were some who did who feared her and didn't know if they should trust her even if they didn't openly show it. Most of those fears had eased over the last month or so but it still lingered there and she couldn't blame them for it. While her seed body had been used as a bait lure and her soul inhabited one of the weapons that defended them, she was still covered by the stigma of being an Angel. She could understand how they felt but it didn't make it hurt any less given that her intentions were anything but malicious. She just wanted to live and experience life and enjoy it with the people she had grown to care about.

As such, she contented herself for the moment in observing the rest of the party goers as she stood by the windows with drink in hand. A _non-alcoholic_ cocktail at that since she had never drank before and was a horrible lightweight in that regard and she had learned that the hard way. Considering what a hangover felt like she wondered why people drank at all. Though, it had been kind of funny when Misato discovered her new body had no alcohol tolerance and she was smashed after a couple of beers. It actually made her reflect on her heavy drinking from before and she was determined not to become that kind of besotted mess again.

Across the room Yui was talking with Ritsuko, Maya, and Misato. Yui had been the one to bring her back to a sense of humanity when she was little more than a beast and she was her guiding light again here in the outside world. She didn't think she could have coped with everything without her, including her own questioning since she came out of the core. She had to hand it to the interrogators, who were currently talking to Fuyutsuki and Kaji. As advertised they were extremely professional. Despite knowing what she was they were completely unbiased when interviewing her. They let the information they gathered from her and others lead them to their conclusions which ultimately led to her being allowed her freedom, although just like everyone else who had been involved at the highest levels of things, she would be kept under some level of observation. She could live with that.

She owed Yui so much and didn't know how to begin to repay her for all that she had done and continued to do for her. Though Yui had needed a little help with a few things too since she had been gone from the outside world for ten years herself and there were some things she wasn't up to speed on either. Misato had helped fill in the gaps and had done so with a great deal of teasing and humour as one would expect. She knew that Misato's antics were also something that she used to heal herself, to get back to normal after everything that had gone on. The ordeal against the Fifteenth had ripped into her hard just as it had Shinji but she was continuing to heal from that everyday and a return to her usual ways helped. She teased people because she cared about them and a laugh and a smile was better than frowning and brooding.

As she liked to do when observing others she opened up her senses so she could feel the nature of their souls and better gauge their moods and state of mind. Misato had a sense of relief about her as she reconnected with her friend Ritsuko, while the doctor herself shared some of that same feeling, she also still felt unsure and anxious. She was finding it to be a tough battle to forgive herself for the things she had been a part of and still saw herself as more perpetrator than victim. She was both of course but she had yet to be able to accept that the vast majority of the things she had done were due to being under Gendo's control. He had known exactly which buttons to push to tie her to him and make her do as he wished.

It was a good thing that she had Maya to lean on and the younger woman's resolve and support of her was ironclad and unwavering and her affection for Ritsuko made her soul light up like a beacon. She was growing, showing a strength and resolve that she never knew she had and was gradually leaving behind the timidness that she had carried for the majority of her life. She would make sure that Ritsuko got through this and she was determined to see the damaged woman be happy and she would do whatever she could to make that happen. She would have an ally there in Misato since she knew from the many conversations that they had in the core that she wanted her old friend to get back to feeling some of that same joy and happiness that she had felt when they were in college. Gendo Ikari and his control over her was gone. It was time to start fresh.

She looked over across the room where others had taken up a spot by the windows, namely the two wounded SIS operatives. The pair were both dressed in the standard blue dress uniforms of the UN forces, though they had forgone the suit jackets. Lake's arm and leg were still in casts and Riker was sitting next to her in his wheelchair, the doctors having yet to give him clearance to be rid of it. A day and a half after he woke up he was knocked flat by an infection for better than a week. He insisted he was strong enough to get around on his own but the doctors weren't willing to let that happen just yet and he had been further overruled by both his partner, their blonde friend from Germany, and the Colonel.

They were talking quietly as they watched the sun begin to set, the peacefulness of the scene belying the blood and thunder she felt in their souls both from battles past and those yet to come. Despite their frayed edges and the scars of loss, their souls had an almost frightening strength in them. They were also deeply intertwined and that brought a smile to her face. They were exactly who they each needed in their life and at some point they were going to fully realize that and the light of their souls would burn even brighter than it already did.

She was also glad that once they were healthy and back on duty that they would be the ones to watch over NERV and the city, taking the fight to the criminal elements and cultists that wanted to prey upon the healing wounds of Tokyo 3. Hostile foreign elements would also no doubt try to gain a foothold to watch NERV and try to make inroads to either gather or steal information or do harm. She almost felt sorry for all of them because they would have no idea what they were going to be facing in these two and whoever stood to fight at their side.

A slight commotion caught her attention and she smiled again when she saw the cause. The pilots and Mari, loaded down with drinks and snacks courtesy of the restaurant staff were headed to join the two soldiers. A connection had been made between them during the training before the attack and as the two soldiers risked life and limb to escort the pilots to their Evangelions. Having witnessed the explosion that swallowed them up Shinji had been so relieved and happy to find out that they had survived, even if he was extremely worried about the condition they were both in.

Unobtrusively connecting with Rei she listened to a bit of the interaction. Matt cheerfully pointed out that they should take note of the rare sight of Mel in a dress uniform and she retaliated by saying that maybe she would trade his broken down carcass for Shinji. He responded by claiming both Rei and Asuka as her replacement. The ongoing banter had the desired effect of making them all smile though she could see that even through her smile Mari looked like she felt that she was intruding.

The fact that she was with them meant that they were accepting her but it was a slow process. They were pretty shocked to hear who and what she was and that she had been here all along and had the power to stop all of it. Being who she was it was easier for her to understand why Mari had not been allowed to intervene and she did her best to explain it to them. But they had been on the sharp end of things and had suffered greatly for years and they needed time to take it in and think about it for themselves. She reminded them though to take into account that Mari herself was one of Kiel's victims and that it had to have been very hard for her to follow her orders rather than step in and end the problem as soon as she could.

The pilots may have been damaged but they weren't stupid and they actually sat down and discussed it among themselves and they recognized the similarities between them and her. She had been used and abused and for far longer than any of them could even imagine and all she really wanted now that she was free of Kiel and had a life and a purpose, was to live that life, make friends, and just be something close to a normal girl. She just wanted to belong somewhere, just like the others did. It was taking a little time but she was getting there and she was gaining their trust and their friendship.

As for the Children, Asuka was making slow but steady progress. Her actions towards Rei and the turning inside out and upside down of everything she had thought and believed had placed her on a long road to not only recovery but of self discovery. The fall out from the incident with Rei had forever changed who she was and knowing the truth about things now had pretty much erased everything that she had been. She was virtually a clean slate now and that presented a daunting future for her. But she had support. In their own ways the other three were all in the same boat to varying degrees, with perhaps Rei and Mari being the most able to identify with what she was going through. She would have to build a new life for herself and hopefully this time she would be able to do so without burning everything in her wake and moving at breakneck speed.

Rei was progressing but it was a slow if not somewhat painful progression at times. Mood swings and emotional outbursts that she didn't understand and withdrawal symptoms from the witch's brew of drugs that she had been taking for so long plagued her, even as she was slowly being weaned off of them. Compounds that may ease one set of symptoms might conflict with something else in her system so it was hard to find anything that would help her. She was determined to fight through it though since she had a much better life ahead of her now and she relied a great deal on Shinji to help her cope. He didn't always know what he should do to try and help her but his presence alone seemed be the best thing for her.

As for Shinji, venting all of his pain and rage during the final battle had taken a lot out of him and he had been the last of them to reawaken after leaving the core. As much as she had hated bringing that out, purging and burning off all of that had probably been good for him in the long run, heading off an inevitable explosion and meltdown at some point. The lingering effect had been in realizing that not all of that rage and pain was directed at his father for all of the ill treatment and indifference of others he had suffered for most of his life.

Realizing that a significant portion of that rage had been directed towards his mother after finding out the truth had been hard for him to deal with. Through talking with Dr. Tokita and the psychologist that had arrived with the SIS investigators, he realized that some of that anger had actually been rooted in her 'death'. While a great deal of it grew and revolved around his father abandoning him, some of it came from a sense of being abandoned by her. Being so young at the time meant he had no ability or to rationalize it. As his young life continued in a downward spiral his child's mind went through the usual thought processes of one so young losing someone so important.

Death was a concept he didn't yet understand so it was more a sense of his mother leaving him. Did he make her leave? Did he do something to make his father so angry that he sent him away? Buried deep underneath everything that happened to him until they were reunited was the root seed that his misery all started the moment she was gone. It was irrational to place the blame there but there it was. Finding out the reasons for her leaving his life had uncovered that particular bomb and lit the fuse. As usual he kept that anger suppressed and his love for Yui and his relief of having her back in his life helped keep the truth of his anger with her hidden from him or at least compartmentalized in a place where he didn't have to confront it.

He felt ashamed to be angry with her. Part of him felt that he had a right to be and another part of him was sickened by it, that he must be a horrible son for feeling that way. Yui couldn't blame him for feeling that way because she felt that he was right, that he had every reason to be angry with her. She was so afraid that her actions would cost her her son just when she had gotten to be with him again and Shinji worried that he would push her away because he had been angry. Even now he still feared that he would find himself alone again.

Their relationship wasn't strained by it, but it was awkward. All of the actual feelings of rage and anger had been burnt out of him and he instinctively knew that Yui had seen and felt it all during her link with them. Some part of his mind had registered her presence through the haze of their berserker state. The biggest issue of it for him now was accepting that what he had been feeling was not abnormal or even unwarranted even though it had been directed toward someone that he loved so much. Time would heal the awkwardness between him and Yui as they moved forward. With the help of the psychologists it was slowly being resolved and he was finally starting to recover. The love and support of those around him helped and the fact that Rei was relying on him was also a positive and gave him something else to focus on as well.

Misato tried to spend as much time with him as she could and they were continuing to work out the kinks from being subjected so intimately to each others memories and feelings. It was killing the woman to not be able to show her true affections for him publicly. Part of her wanted the world to know how much she loved and cared for Shinji, but that same revelation was not exactly socially acceptable considering the differences in their age. Once he was older it would be much less of a problem but it preyed upon her insecurities. The heart and the soul may know what it wanted and what pieces fit where, but in the real physical world that wasn't always an easy thing.

As for herself she found the nature of her feelings about Shinji to be a little confusing. There was no doubt that she indeed loved him, how could she not love a soul such as his? But what form that love would take and what it would become seemed a little unclear. Even though she was a Seed of Life, she was not unfamiliar with love but she lacked experience with relationships and how the two meshed together at their varying levels. During her time in the core she had grown to love Yui as the closest of friends and over time as loneliness and despair washed over them they became more than that, giving each other comfort and pleasure both emotionally and physically and she was sure it had prevented them both from going mad.

She supposed that in time things would find their own level and that it was far too soon to be worrying about such things and their were other pressing matters that would need to be taken care of first, namely creating an identity for herself. Currently, herself and Mari fell into the same category as Yui did upon returning from her ten year absence. Top Secret and Need To Know were handy elements and gave them time to create an identity for them both and there were already some ideas in the works. Thus far it had been agreed that she would take on the last name of Makinami and be listed as Mari's guardian since she would need one. A story was being considered where she would be a coworker of Yui's, that her 'accident ' with Unit 01 had been sabotage and she had been placed in hiding along with her due to threats being made upon them and they had only recently been able to resurface into society. It was in the early stages of its creation but eventually they would have a complete profile for her that could be utilized when it was necessary.

There was also something in the works to create a similar scenario in regards to Asuka's mother if they were able to remove her from Unit 02. That however was probably going to be a lengthy process if they could accomplish it at all and Yui and Ritsuko were already exploring options. One thing that was certain was that they would have to keep testing with Unit 02, having Asuka make continued contact with Kyoko. Drawing her out into more contact with her daughter and discovering more of the nature of the red Eva's resident consciousness would help them formulate methods for getting her out. They had to both loosen the resident consciousness's hold on her and get her to want to leave.

Reconnecting with her daughter would help that and if all else failed they could always take her out forcibly, but there was always a risk of causing further damage to her soul. With Unit 02 being made from Adam she couldn't do that, but Mari could and had already offered her help if they needed it. They also needed a body for her soul to migrate to. Any form of soul transference like was utilized to move Rei's soul between bodies would not work. There was too much risk that the Eva's consciousness would try to latch onto Kyoko's soul and go with her. An actual body constructed with her own DNA in the plug would be a better scenario and they would have greater control and better be able to separate the two entities. Just as with Lilith's own old seed body, the soul permeated every single spec of a person's being. There would be a minuscule trace of Kyoko's soul attached to the sample and it would grow within the clone and act like a beacon and given the absolute territory of the soul, it would be much harder for the core consciousness to try and follow.

If Kyoko couldn't form a body for herself from the LCL on her transition out, that meant that a body really would be needed to be cloned for her and that was likely their best chance for success anyway. Problem was cloning was highly illegal but their was really no other option. They should be able to secure a DNA sample for Kyoko since there should be one on file at NERV Berlin. If not, then they would have to try and utilize Asuka's DNA to make her a body. None of this had been discussed with Asuka yet, more planning and groundwork needed to be done and she needed to have more time to recover before it was presented to her. One thing was certain though, they would be doing their utmost to retrieve Kyoko from Unit 02. Not trying wasn't even a consideration. They were determined to give Asuka back her mother.

Yui walked up to her, a soft smile on her face. "Engaging in your favourite hobby of observing everyone?"

"Can't help it," she responded. "Especially when I feel joy and hope in them."

"There hasn't been much of that for a long time," Yui lamented. "Not even for us, but now that all of the world destroying threats are gone it's like we had been all holding our breath and can now finally breathe again."

"So much has changed for them," Lilith commented, looking at the pilots. "In such a short time their lives have turned completely around."

"It's hard to believe that with everything they've been through and everything they've learned that they are even able to progress they way they have," Yui said. "I know it hasn't been easy for them by any definition, but it could be so much harder than it has been."

"Resiliency seems to be the human way," Lilith mused. "So long as there is just a little bit of effort in it and a desire to be something other than a victim, one can continue to move forward."

"You know what they say," Misato said as she made her presence known. "What doesn't kill you makes you stronger. In which case we should all be like Superman by now," she added cheekily.

"Who?" Lilith asked, confused.

"I'll explain it later," the purplenette said airily waving her hand. She kind of enjoyed confusing Lilith like that. She smiled. "It's nice to see him like that isn't it?" She was referring to Shinji who even though he still had a shy air about him, was smiling and even laughing a little at something Captain Lake said to him as she offered him a Sharpie to sign the cast on her arm with. Captain Riker said something that got the girls giggling and Lake gave him the finger, though she was smiling as well.

"It is," Yui agreed. There was no better sight to her than to see a genuine smile on her son's face. "And I'm going to make sure that smile stays there too. I'll do whatever it takes to make sure he's never sad or lonely again and that he knows he's loved."

Lilith took her hand and Misato placed a hand on her shoulder. "Don't think that will be a problem," Misato said as they continued to watch him and the others. "You'll have plenty of help to make sure of that."

* * *

Please leave a review if you would be so kind.

And while you're here, check out my other stories.

I am never really entirely happy with the endings I come up with, but, there it is. Glad to finally be done with this after all of the trouble I had over the last couple of years as I slogged to finish this. Not all of those problems were related to the writing, they were mostly personal and depression (or something close to it) related, but certainly did impact it. I got sick to death of falling into those dark little holes then trying to crawl out. Writing is one thing that is supposed to help me with that but in this case it made this fic seem like the story that would never end.

But, no one wants to hear about my shit. I hope this story was entertaining for most of you...I know there were a couple of ignorant trolls who would say otherwise but I'm pretty sure I don't give a shit about the opinion of an ignorant troll.

Now I can completely turn all of my attention to whatever the hell I'm going to do with A Chance Encounter and Lonely Exile. And whatever else happens along. I do have another multi-chapter thing sitting in dry dock that I started at the same time as this one. Maybe I'll get at it too.


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